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Arnal G, Attia MA, Asohan J, Lei Z, Golisch B, Brumer H. A Low-Volume, Parallel Copper-Bicinchoninic Acid (BCA) Assay for Glycoside Hydrolases. Methods Mol Biol 2023; 2657:3-14. [PMID: 37149519 DOI: 10.1007/978-1-0716-3151-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The quantitation of liberated reducing sugars by the copper-bicinchoninic acid (BCA) assay provides a highly sensitive method for the measurement of glycoside hydrolase (GH) activity, particularly on soluble polysaccharide substrates. Here we describe a straightforward method adapted to low-volume polymerase chain reaction (PCR) tubes that enables the rapid, parallel determination of GH kinetics in applications ranging from initial activity screening and assay optimization to precise Michaelis-Menten analysis.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Jathavan Asohan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Zhenhuan Lei
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Benedikt Golisch
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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Abstract
α-Glucan is a major cell wall component and a virulence and adhesion factor for fungal cells. However, the biosynthetic pathway of α-glucan was still unclear. α-Glucan was shown to be composed mainly of 1,3-glycosidically linked glucose, with trace amounts of 1,4-glycosidically linked glucose. Besides the α-glucan synthetases, amylase-like proteins were also important for α-glucan synthesis. In our previous work, we showed that Aspergillus nidulans AmyG was an intracellular protein and was crucial for the proper formation of α-glucan. In the present study, we expressed and purified AmyG in an Escherichia coli system. Enzymatic characterization found that AmyG mainly functioned as an α-amylase that degraded starch into maltose. AmyG also showed weak glucanotransferase activity. Most intriguingly, supplementation with maltose in shaken liquid medium could restore the α-glucan content and the phenotypic defect of a ΔamyG strain. These data suggested that AmyG functions mainly as an intracellular α-amylase to provide maltose during α-glucan synthesis in A. nidulans. IMPORTANCE Short α-1,4-glucan was suggested as the primer structure for α-glucan synthesis. However, the exact structure and its source remain elusive. AmyG was essential to promote α-glucan synthesis and had a major impact on the structure of α-glucan in the cell wall. Data presented here revealed that AmyG belongs to the GH13_5 family and showed strong amylase function, digesting starch into maltose. Supplementation with maltose efficiently rescued the phenotypic defect and α-glucan deficiency in an ΔamyG strain but not in an ΔagsB strain. These results provide the first piece of evidence for the primer structure of α-glucan in fungal cells, although it might be specific to A. nidulans.
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Abstract
The quantitation of liberated reducing sugars by the copper-bicinchoninic acid (BCA) assay provides a highly sensitive method for the measurement of glycoside hydrolase (GH) activity, particularly on soluble polysaccharide substrates. Here, we describe a straightforward method adapted to low-volume polymerase chain reaction (PCR) tubes which enables the rapid, parallel determination of GH kinetics in applications ranging from initial activity screening and assay optimization, to precise Michaelis-Menten analysis.
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Medium-throughput profiling method for screening polysaccharide-degrading enzymes in complex bacterial extracts. J Microbiol Methods 2012; 89:222-9. [PMID: 22465222 DOI: 10.1016/j.mimet.2012.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/06/2012] [Accepted: 03/06/2012] [Indexed: 01/26/2023]
Abstract
Polysaccharides are the most abundant and the most diverse renewable materials found on earth. Due to the stereochemical variability of carbohydrates, polysaccharide-degrading enzymes - i.e. glycoside hydrolases and polysaccharide lyases - are essential tools for resolving the structure of these complex macromolecules. The exponential increase of genomic and metagenomic data contrasts sharply with the low number of proteins that have ascribed functions. To help fill this gap, we designed and implemented a medium-throughput profiling method to screen for polysaccharide-degrading enzymes in crude bacterial extracts. Our strategy was based on a series of filtrations, which are absolutely necessary to eliminate any reducing sugars not directly generated by enzyme degradation. In contrast with other protocols already available in the literature, our method can be applied to any panel of polysaccharides having known and unknown structures because no chemical modifications are required. We applied this approach to screen for enzymes that occur in Pseudoalteromonas carrageenovora grown in two culture conditions.
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Beldman G, Vincken JP, Schols HA, Meeuwsen PJA, Herweijer M, Voragen AGJ. Degradation of Differently Substituted Xylogalacturonans by Endoxylogalacturonan Hydrolse and Endopolygalacturonases. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001618546] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Firozi P, Zhang W, Chen L, Quiocho FA, Worley KC, Templeton NS. Identification and removal of colanic acid from plasmid DNA preparations: implications for gene therapy. Gene Ther 2010; 17:1484-99. [PMID: 20664542 DOI: 10.1038/gt.2010.97] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polysaccharide contaminants in plasmid DNA, including current good manufacturing practices (cGMP) clinical preparations, must be removed to provide the greatest safety and efficacy for use in gene therapy and other clinical applications. We developed assays and methods for the detection and removal of these polysaccharides, our Super Clean DNA (SC-DNA) process, and have shown that these contaminants in plasmid DNA preparations are responsible for toxicity observed post-injection in animals. Furthermore, these contaminants limit the efficacy of low and high doses of plasmid DNA administered by numerous delivery routes. In particular, colanic acid (CA) that is mainly long-chained, branched and has high molecular weight (MW) is most refractory when complexed to cationic delivery vehicles and injected intravenously (IV). Because CA is often extremely large and tightly intertwined with DNA, it must be degraded, in order, to be effectively removed. We have produced a recombinant, truncated colanic acid degrading enzyme (CAE) that successfully accomplishes this task. Initially, we isolated a newly identified CAE from a bacteriophage that required truncation for proper folding while retaining its full enzymatic activity during production. Any plasmid DNA preparation can be digested with CAE and further purified, providing a critical advance to non-viral gene therapy.
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Affiliation(s)
- P Firozi
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
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Rigouin C, Ladrat CD, Sinquin C, Colliec-Jouault S, Dion M. Assessment of biochemical methods to detect enzymatic depolymerization of polysaccharides. Carbohydr Polym 2009. [DOI: 10.1016/j.carbpol.2008.10.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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van der Kaaij RM, Janeček Š, van der Maarel MJEC, Dijkhuizen L. Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal alpha-amylase enzymes. MICROBIOLOGY-SGM 2008; 153:4003-4015. [PMID: 18048915 DOI: 10.1099/mic.0.2007/008607-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Currently known fungal alpha-amylases are well-characterized extracellular enzymes that are classified into glycoside hydrolase subfamily GH13_1. This study describes the identification, and phylogenetic and biochemical analysis of novel intracellular fungal alpha-amylases. The phylogenetic analysis shows that they cluster in the recently identified subfamily GH13_5 and display very low similarity to fungal alpha-amylases of family GH13_1. Homologues of these intracellular enzymes are present in the genome sequences of all filamentous fungi studied, including ascomycetes and basidiomycetes. One of the enzymes belonging to this new group, Amy1p from Histoplasma capsulatum, has recently been functionally linked to the formation of cell wall alpha-glucan. To study the biochemical characteristics of this novel cluster of alpha-amylases, we overexpressed and purified a homologue from Aspergillus niger, AmyD, and studied its activity product profile with starch and related substrates. AmyD has a relatively low hydrolysing activity on starch (2.2 U mg(-1)), producing mainly maltotriose. A possible function of these enzymes in relation to cell wall alpha-glucan synthesis is discussed.
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Affiliation(s)
- R M van der Kaaij
- Centre for Carbohydrate Bioprocessing, TNO-University of Groningen, Haren, The Netherlands.,Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Š Janeček
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - M J E C van der Maarel
- Business Unit Food and Biotechnology Innovations, TNO Quality of Life, Groningen, The Netherlands.,Centre for Carbohydrate Bioprocessing, TNO-University of Groningen, Haren, The Netherlands.,Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - L Dijkhuizen
- Centre for Carbohydrate Bioprocessing, TNO-University of Groningen, Haren, The Netherlands.,Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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van der Kaaij RM, Yuan XL, Franken A, Ram AFJ, Punt PJ, van der Maarel MJEC, Dijkhuizen L. Two novel, putatively cell wall-associated and glycosylphosphatidylinositol-anchored alpha-glucanotransferase enzymes of Aspergillus niger. EUKARYOTIC CELL 2007; 6:1178-88. [PMID: 17496125 PMCID: PMC1951109 DOI: 10.1128/ec.00354-06] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In the genome sequence of Aspergillus niger CBS 513.88, three genes were identified with high similarity to fungal alpha-amylases. The protein sequences derived from these genes were different in two ways from all described fungal alpha-amylases: they were predicted to be glycosylphosphatidylinositol anchored, and some highly conserved amino acids of enzymes in the alpha-amylase family were absent. We expressed two of these enzymes in a suitable A. niger strain and characterized the purified proteins. Both enzymes showed transglycosylation activity on donor substrates with alpha-(1,4)-glycosidic bonds and at least five anhydroglucose units. The enzymes, designated AgtA and AgtB, produced new alpha-(1,4)-glycosidic bonds and therefore belong to the group of the 4-alpha-glucanotransferases (EC 2.4.1.25). Their reaction products reached a degree of polymerization of at least 30. Maltose and larger maltooligosaccharides were the most efficient acceptor substrates, although AgtA also used small nigerooligosaccharides containing alpha-(1,3)-glycosidic bonds as acceptor substrate. An agtA knockout of A. niger showed an increased susceptibility towards the cell wall-disrupting compound calcofluor white, indicating a cell wall integrity defect in this strain. Homologues of AgtA and AgtB are present in other fungal species with alpha-glucans in their cell walls, but not in yeast species lacking cell wall alpha-glucan. Possible roles for these enzymes in the synthesis and/or maintenance of the fungal cell wall are discussed.
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Affiliation(s)
- R M van der Kaaij
- Centre for Carbohydrate Bioprocessing, TNO-University of Groningen, Haren, The Netherlands
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Verhoef R, Beldman G, Schols HA, Siika-aho M, Rättö M, Buchert J, Voragen AGJ. Characterisation of a 1,4-beta-fucoside hydrolase degrading colanic acid. Carbohydr Res 2005; 340:1780-8. [PMID: 15993389 DOI: 10.1016/j.carres.2005.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 04/27/2005] [Accepted: 06/07/2005] [Indexed: 10/25/2022]
Abstract
A novel colanic acid-degrading enzyme was isolated from a mixed culture filtrate obtained by enrichment culturing of a compost sample using colanic acid as carbon source. The enzyme was partially purified resulting in a 17-fold increase in specific activity. Further purification by Native PAGE revealed that the enzyme is part of a high-molecular weight multi protein complex of at least six individual proteins. The enzyme showed a temperature optimum at 50 degrees C while after 5h at 50 degrees C and pH7 still 70% of the total activity was left. The pH optimum was found to be pH7. Analysis of the degradation products showed that the enzyme is a novel 1,4-beta-fucoside hydrolase that liberates repeating units of colanic acid with varying degrees of acetylation. Km and Vmax of the enzyme were determined against the native substrate as well as its de-O-acetylated and depyruvated forms. Compared to the native substrate the affinity of the enzyme for the modified substrates was much lower. However, for the de-O-acetylated sample a dramatic increase in catalytic efficiency was observed. The native form of the substrate showed substrate inhibition at high concentrations, probably due to the formation of nonproductive substrate complexes. Removal of the acetyl groups probably prevents this effect resulting in a higher catalytic efficiency.
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Affiliation(s)
- René Verhoef
- Wageningen University, Department of Agrotechnology and Food Sciences, Laboratory of Food Chemistry, Bomenweg 2, 6703 HD Wageningen, The Netherlands
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Hussain H, Mant A, Seale R, Zeeman S, Hinchliffe E, Edwards A, Hylton C, Bornemann S, Smith AM, Martin C, Bustos R. Three isoforms of isoamylase contribute different catalytic properties for the debranching of potato glucans. THE PLANT CELL 2003; 15:133-49. [PMID: 12509527 PMCID: PMC143484 DOI: 10.1105/tpc.006635] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2002] [Accepted: 10/24/2002] [Indexed: 05/17/2023]
Abstract
Isoamylases are debranching enzymes that hydrolyze alpha-1,6 linkages in alpha-1,4/alpha-1,6-linked glucan polymers. In plants, they have been shown to be required for the normal synthesis of amylopectin, although the precise manner in which they influence starch synthesis is still debated. cDNA clones encoding three distinct isoamylase isoforms (Stisa1, Stisa2, and Stisa3) have been identified from potato. The expression patterns of the genes are consistent with the possibility that they all play roles in starch synthesis. Analysis of the predicted sequences of the proteins suggested that only Stisa1 and Stisa3 are likely to have hydrolytic activity and that there probably are differences in substrate specificity between these two isoforms. This was confirmed by the expression of each isoamylase in Escherichia coli and characterization of its activity. Partial purification of isoamylase activity from potato tubers showed that Stisa1 and Stisa2 are associated as a multimeric enzyme but that Stisa3 is not associated with this enzyme complex. Our data suggest that Stisa1 and Stisa2 act together to debranch soluble glucan during starch synthesis. The catalytic specificity of Stisa3 is distinct from that of the multimeric enzyme, indicating that it may play a different role in starch metabolism.
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Affiliation(s)
- Hasnain Hussain
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
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van der Vlugt-Bergmans CJ, Meeuwsen PJ, Voragen AG, van Ooyen AJ. Endo-xylogalacturonan hydrolase, a novel pectinolytic enzyme. Appl Environ Microbiol 2000; 66:36-41. [PMID: 10618200 PMCID: PMC91782 DOI: 10.1128/aem.66.1.36-41.2000] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/1999] [Accepted: 10/01/1999] [Indexed: 11/20/2022] Open
Abstract
We screened an Aspergillus tubingensis expression library constructed in the yeast Kluyveromyces lactis for xylogalacturonan-hydrolyzing activity in microwell plates by using a bicinchoninic acid assay. This assay detects reducing carbohydrate groups when they are released from a carbohydrate by enzymatic activity. Two K. lactis recombinants exhibiting xylogalacturonan-hydrolyzing activity were found among the 3,400 colonies tested. The cDNA insert of these recombinants encoded a 406-amino-acid protein, designated XghA, which was encoded by a single-copy gene, xghA. A multiple-sequence alignment revealed that XghA was similar to both polygalacturonases (PGs) and rhamnogalacturonases. A detailed examination of conserved regions in the sequences of these enzymes revealed that XghA resembled PGs more. High-performance liquid chromatography and matrix-assisted laser desorption ionization-time of flight mass spectrometry of the products of degradation of xylogalacturonan and saponified modified hairy regions of apple pectin by XghA demonstrated that this enzyme uses an endo type of mechanism. XghA activity appeared to be specific for a xylose-substituted galacturonic acid backbone.
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Affiliation(s)
- C J van der Vlugt-Bergmans
- Industrial Microbiology Group, Department of Food Technology and Nutritional Sciences, Wageningen Agricultural University, NL-6700 EV Wageningen, The Netherlands.
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