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  • Insights Into Diphthamide, Key Diphtheria Toxin Effector
    Toxins 2013, 5, 958-968; doi:10.3390/toxins5050958 OPEN ACCESS toxins ISSN 2072-6651 www.mdpi.com/journal/toxins Brief Report Insights into Diphthamide, Key Diphtheria Toxin Effector Wael Abdel-Fattah 1,†, Viktor Scheidt 1,†, Shanow Uthman 2, Michael J. R. Stark 3 and Raffael Schaffrath 1,2,* 1 Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel D-34132, Germany; E-Mails: [email protected] (W.A.-F.); [email protected] (V.S.) 2 Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; E-Mail: [email protected] 3 Centre for Gene Regulation & Expression, University of Dundee, Dundee, DD1 5EH, Scotland; E-Mail: [email protected] † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +49-561-804-4175; Fax: +49-561-804-4337. Received: 14 March 2013; in revised form: 17 April 2013 / Accepted: 26 April 2013 / Published: 3 May 2013 Abstract: Diphtheria toxin (DT) inhibits eukaryotic translation elongation factor 2 (eEF2) by ADP-ribosylation in a fashion that requires diphthamide, a modified histidine residue on eEF2. In budding yeast, diphthamide formation involves seven genes, DPH1-DPH7. In an effort to further study diphthamide synthesis and interrelation among the Dph proteins, we found, by expression in E. coli and co-immune precipitation in yeast, that Dph1 and Dph2 interact and that they form a complex with Dph3. Protein-protein interaction mapping shows that Dph1-Dph3 complex formation can be dissected by progressive DPH1 gene truncations. This identifies N- and C-terminal domains on Dph1 that are crucial for diphthamide synthesis, DT action and cytotoxicity of sordarin, another microbial eEF2 inhibitor.
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  • Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications
    Hindawi Publishing Corporation Enzyme Research Volume 2012, Article ID 921362, 14 pages doi:10.1155/2012/921362 Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications Siew Ling Hii,1 Joo Shun Tan,2 Tau Chuan Ling,3 and Arbakariya Bin Ariff4 1 Department of Chemical Engineering, Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, 53300 Kuala Lumpur, Malaysia 2 Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia 3 Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 4 Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia Correspondence should be addressed to Arbakariya Bin Ariff, [email protected] Received 26 March 2012; Revised 12 June 2012; Accepted 12 June 2012 Academic Editor: Joaquim Cabral Copyright © 2012 Siew Ling Hii et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The use of pullulanase (EC 3.2.1.41) has recently been the subject of increased applications in starch-based industries especially those aimed for glucose production. Pullulanase, an important debranching enzyme, has been widely utilised to hydrolyse the α-1,6 glucosidic linkages in starch, amylopectin, pullulan, and related oligosaccharides, which enables a complete and efficient conversion of the branched polysaccharides into small fermentable sugars during saccharification process. The industrial manufacturing of glucose involves two successive enzymatic steps: liquefaction, carried out after gelatinisation by the action of α- amylase; saccharification, which results in further transformation of maltodextrins into glucose.
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  • GRAS Notice 975, Maltogenic Alpha-Amylase Enzyme Preparation
    GRAS Notice (GRN) No. 975 https://www.fda.gov/food/generally-recognized-safe-gras/gras-notice-inventory novozyme~ Rethink Tomorrow A Maltogenic Alpha-Amylase from Geobacillus stearothermophilus Produced by Bacillus licheniformis Janet Oesterling, Regulatory Affairs, Novozymes North America, Inc., USA October 2020 novozyme~ Reth in k Tomorrow PART 2 - IDENTITY, METHOD OF MANUFACTURE, SPECIFICATIONS AND PHYSICAL OR TECHNICAL EFFECT OF THE NOTIFIED SUBSTANCE ..................................................................... 4 2.1 IDENTITY OF THE NOTIFIED SUBSTANCE ................................................................................ 4 2.2 IDENTITY OF THE SOURCE ......................................................................................................... 4 2.2(a) Production Strain .................................................................................................. 4 2.2(b) Recipient Strain ..................................................................................................... 4 2.2(c) Maltogenic Alpha-Amylase Expression Plasmid ................................................... 5 2.2(d) Construction of the Recombinant Microorganism ................................................. 5 2.2(e) Stability of the Introduced Genetic Sequences .................................................... 5 2.2(f) Antibiotic Resistance Gene .................................................................................. 5 2.2(g) Absence of Production Organism in Product ......................................................
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  • Application A1204 Βeta-Amylase from Soybean (Glycine Max)
    OFFICIAL 27 October 2020 [139-20] Supporting document 1 Risk and Technical assessment – Application A1204 Βeta-amylase from soybean (Glycine max) as a processing aid (enzyme) Executive summary The purpose of the application is to amend Schedule 18 – Processing Aids of the Australia New Zealand Food Standards Code (the Code) to include the enzyme beta-amylase (β- amylase) (EC 3.2.1.2) produced from soybeans (Glycine max). β-Amylase is proposed as a processing aid in starch processing for the production of maltose syrup. The evidence presented to support the proposed use of the enzyme provides adequate assurance that the enzyme, in the quantity and form proposed to be used, is technologically justified and has been demonstrated to be effective in achieving its stated purpose. The enzyme meets international identity and purity specifications. β-Amylase from soybean is derived from the edible parts of the Glycine max plant, for which a history of safe use over generations is well known. FSANZ considers that soybean β-amylase is unlikely to pose an allergenicity concern. Bioinformatic analysis identified a degree of amino acid sequence homology between β- amylase from soybean and an allergenic protein from wheat, but FSANZ does not consider β-amylase to be of allergenic concern in wheat allergic individuals given the likely very low exposure and that the enzyme is likely to be digested in the stomach like other dietary proteins. The WHO/IUIS Allergen Nomenclature Database lists seven soy proteins that are food allergens. β-amylase from soybean is not one of these seven allergenic soy proteins and is not an allergen to individuals with soybean food allergy.
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  • Characterization of Starch Debranching Enzymes of Maize Endosperm Afroza Rahman Iowa State University
    Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1998 Characterization of starch debranching enzymes of maize endosperm Afroza Rahman Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Biochemistry Commons, Molecular Biology Commons, and the Plant Sciences Commons Recommended Citation Rahman, Afroza, "Characterization of starch debranching enzymes of maize endosperm " (1998). Retrospective Theses and Dissertations. 12519. https://lib.dr.iastate.edu/rtd/12519 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps.
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  • Production of a Thermostable Pullulanase by a Thermus Sp
    38 J. Jpn. Soc. Starch Sci., Vol. 34, No. 1, p. 38•`44 (1987)•l Production of a Thermostable Pullulanase by a Thermus sp. Nobuyuki NAKAMURA,* Nobuhiro SASHIHARA,** Hiromi NAGAYAMA and Koki HORIKOSHI*** Laboratory of Bacterial Metabolism, The Superbugs Project, Research Development Corporation of Japan (2-28-8, Honkomagome, Bunkyo-ku, Tokyo 113, Japan) (Received November 29, 1986) A moderate thermophile that produces a large amount of extracellular pullulanase was isolated from soil. The isolate (AMD-33), that grew at 37 to 74•Ž with an optimum at 65•Ž, was identified as a Thermus sp. strain. Maximal enzyme production was attained after 3 days shaking cultivation at 60•Ž on a medium composed of 1% pullulan, 2% gelatin, 0.1% K2HPO4, 0.03% MgSO4•E7H2O and 0.25% CaCO3. Pullulanase synthesis was enhanced by pullulan, soluble starch and dextrin as well as maltose but not at all by glucose. The enzyme, which was most active at pH 5.5-5.7 and 70 , was stabilized by Ca2+, and the optimum temperature for activity shifted to 75•Ž in the presence of 3mM CaCl2. Pullulanase (pullulan 6-glucanohydrolase, EC grow during the processes and interfere with 3. 2. 1. 41) is a debranching enzyme which the saccharification. Accordingly, active and specifically cleaves the ƒ¿-1, 6-glucosidic linkages thermostable amylolytic enzymes will be very in pullulan and amylopectin. This enzyme is important for the starch processing industry. commercially produced using bacteria1•`5) and Although some mesophilic and thermophilic is generally used in combination with several bacteria which produce significant amounts of amylases such as glucoamylases, ƒ¿-amylases, pullulanases have been reported, 8,11•`18) little is ƒÀ-amylases and maltooligosaccharides-forming known about the formation and biochemical enzymes for the production of glucose, maltose characteristics of pullulanases from Gram and some related starch conversion syrups, negative thermophiles except for the cell because it improves the saccharification rates associated enzyme from T.
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  • Genes for Degradation and Utilization of Uronic Acid-Containing Polysaccharides of a Marine Bacterium Catenovulum Sp
    Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4 Go Furusawa, Nor Azura Azami and Aik-Hong Teh Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia ABSTRACT Background. Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. Methods. To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. Results. The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in Submitted 5 August 2020 the QB4 genome based on the CAZy database.
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  • Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications
    Hindawi Publishing Corporation Enzyme Research Volume 2012, Article ID 921362, 14 pages doi:10.1155/2012/921362 Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications Siew Ling Hii,1 Joo Shun Tan,2 Tau Chuan Ling,3 and Arbakariya Bin Ariff4 1 Department of Chemical Engineering, Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, 53300 Kuala Lumpur, Malaysia 2 Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia 3 Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 4 Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia Correspondence should be addressed to Arbakariya Bin Ariff, [email protected] Received 26 March 2012; Revised 12 June 2012; Accepted 12 June 2012 Academic Editor: Joaquim Cabral Copyright © 2012 Siew Ling Hii et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The use of pullulanase (EC 3.2.1.41) has recently been the subject of increased applications in starch-based industries especially those aimed for glucose production. Pullulanase, an important debranching enzyme, has been widely utilised to hydrolyse the α-1,6 glucosidic linkages in starch, amylopectin, pullulan, and related oligosaccharides, which enables a complete and efficient conversion of the branched polysaccharides into small fermentable sugars during saccharification process. The industrial manufacturing of glucose involves two successive enzymatic steps: liquefaction, carried out after gelatinisation by the action of α- amylase; saccharification, which results in further transformation of maltodextrins into glucose.
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  • A Pullulanase Enzyme Preparation from a Recombinant Strain of Bacillus Licheniformis
    A Pullulanase Enzyme Preparation from a recombinant strain of Bacillus licheniformis PROCESSING AID APPLICATION Food Standards Australia New Zealand Applicant: DUPONT AUSTRALIA PTY LTD Submitted by: AXIOME PTY LTD May 17, 2018 Processing Aid Application Pullulanase CONTENTS: 1. General information ................................................................................................................. 2 1.1 Applicant details ................................................................................................................ 2 1.2 Purpose of the application ................................................................................................. 3 1.3 Justification for the application ......................................................................................... 3 1.4 Support for the application ................................................................................................ 4 1.5 Assessment procedure ....................................................................................................... 4 1.6 Confidential Commercial Information .............................................................................. 4 1.7 Exclusive capturable commercial benefit (ECCB) ........................................................... 4 1.8 International and other National Standards ....................................................................... 4 1.9 Statutory declaration ........................................................................................................
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  • Production of Neoagaro-Oligosaccharides With Various Degrees Of
    ORIGINAL RESEARCH published: 24 September 2020 doi: 10.3389/fmicb.2020.574771 Production of Neoagaro- Oligosaccharides With Various Degrees of Polymerization by Using a Truncated Marine Agarase Wu Qu1, Dingquan Wang1, Jie Wu 2, Zhuhua Chan 2, Wenjie Di 2, Jianxin Wang1 and Runying Zeng 2,3* 1Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China, 2 Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China, 3 Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen, China Bioactivities, such as freshness maintenance, whitening, and prebiotics, of marine neoagaro-oligosaccharides (NAOS) with 4–12 degrees of polymerization (DPs) have been proven. However, NAOS produced by most marine β-agarases always possess low DPs (≤6) and limited categories; thus, a strategy that can efficiently produce NAOS especially Edited by: with various DPs ≥8 must be developed. In this study, 60 amino acid residues with no Obulisamy Parthiba Karthikeyan, functional annotation result were removed from the C-terminal of agarase AgaM1, and University of Houston, truncated recombinant AgaM1 (trAgaM1) was found to have the ability to produce NAOS United States with various DPs (4–12) under certain conditions. The catalytic efficiency and stability of Reviewed by: Kris Niño Gomez Valdehuesa, trAgaM1 were obviously lower than the wild type (rAgaM1), which probably endowed The University of Manchester, trAgaM1 with the ability to produce NAOS with various DPs. The optimum conditions for United Kingdom Xiaoqiang Ma, various NAOS production included mixing 1% agarose (w/v) with 10.26 U/ml trAgaM1 Singapore-MIT Alliance for Research and incubating the mixture at 50°C in deionized water for 100 min.
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  • Identification of Functionally Related Enzymes by Learning-To-Rank Methods
    Identification of functionally related enzymes by learning-to-rank methods Michiel Stock, Thomas Fober, Eyke H¨ullermeier,Serghei Glinca, Gerhard Klebe, Tapio Pahikkala, Antti Airola, Bernard De Baets, Willem Waegeman ∗ Abstract Enzyme sequences and structures are routinely used in the biological sciences as queries to search for func- tionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes. 1 Introduction Modern high-throughput technologies in molecular biology are generating more and more protein sequences and ter- tiary structures, of which only a small fraction can ever be experimentally annotated w.r.t.
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  • Supplementary Material Toxicological Impacts and Likely Protein Targets Of
    Supplementary Material Toxicological impacts and likely protein targets of bisphenol A in Paramecium caudatum Marcus V. X. Senra† & Ana Lúcia Fonseca Instituto de Recursos Naturais, Universidade Federal de Itajubá, 37500-903, Itajubá, Minas Gerais – Brazil †To whom correspondence should be addressed – [email protected]; Orcid - 0000-0002-3866- 8837 Table S1. Annotation data on the P. caudatum 3D modelled proteins and their binding energies to BPA. BINDING ID DESCRIPTION CHROMOSOME NT_START NT_END ENERGIES (kcal/mol) PCAU.43c3d.1.P00010012 Tryptophan synthase beta subunit-like PLP-dependent enzyme scaffold_0001 23197 24853 -7.4 PCAU.43c3d.1.P00010015 Ribosomal protein L32e scaffold_0001 26373 26859 -6.2 PCAU.43c3d.1.P00010044 Catalase, mono-functional, haem-containing scaffold_0001 71821 73367 -6.5 PCAU.43c3d.1.P00010050 Dihydroorotate dehydrogenase, class 1/ 2 scaffold_0001 76614 79650 -6.6 PCAU.43c3d.1.P00010054 Serine/threonine/dual specificity protein kinase, catalytic domain scaffold_0001 83399 84653 -6.7 PCAU.43c3d.1.P00010070 Peptidyl-prolyl cis-trans isomerase, FKBP-type scaffold_0001 104909 105387 -5.9 PCAU.43c3d.1.P00010103 V-ATPase proteolipid subunit C-like domain scaffold_0001 168736 169346 -5.6 PCAU.43c3d.1.P00010112 DNA-directed RNA polymerase, RBP11-like dimerisation domain scaffold_0001 180310 181372 -6.0 PCAU.43c3d.1.P00010165 Vacuolar (H+)-ATPase G subunit scaffold_0001 252653 253112 -5.6 PCAU.43c3d.1.P00010176 Coproporphyrinogen III oxidase, aerobic scaffold_0001 262051 263168 -6.7 PCAU.43c3d.1.P00010205 Metalloenzyme,
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