Enzymes and Beermaking Streamlining Enzyme Analysis in Brewing
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METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0. -
Increasing the Amylose Content of Durum Wheat Through Silencing of the Sbeiia Genes
Sestili et al. BMC Plant Biology 2010, 10:144 http://www.biomedcentral.com/1471-2229/10/144 RESEARCH ARTICLE Open Access IncreasingResearch article the amylose content of durum wheat through silencing of the SBEIIa genes Francesco Sestili1, Michela Janni1, Angela Doherty2, Ermelinda Botticella1, Renato D'Ovidio1, Stefania Masci1, Huw D Jones2 and Domenico Lafiandra*1 Abstract Background: High amylose starch has attracted particular interest because of its correlation with the amount of Resistant Starch (RS) in food. RS plays a role similar to fibre with beneficial effects for human health, providing protection from several diseases such as colon cancer, diabetes, obesity, osteoporosis and cardiovascular diseases. Amylose content can be modified by a targeted manipulation of the starch biosynthetic pathway. In particular, the inactivation of the enzymes involved in amylopectin synthesis can lead to the increase of amylose content. In this work, genes encoding starch branching enzymes of class II (SBEIIa) were silenced using the RNA interference (RNAi) technique in two cultivars of durum wheat, using two different methods of transformation (biolistic and Agrobacterium). Expression of RNAi transcripts was targeted to the seed endosperm using a tissue-specific promoter. Results: Amylose content was markedly increased in the durum wheat transgenic lines exhibiting SBEIIa gene silencing. Moreover the starch granules in these lines were deformed, possessing an irregular and deflated shape and being smaller than those present in the untransformed controls. Two novel granule bound proteins, identified by SDS- PAGE in SBEIIa RNAi lines, were investigated by mass spectrometry and shown to have strong homologies to the waxy proteins. RVA analysis showed new pasting properties associated with high amylose lines in comparison with untransformed controls. -
Product Guide
www.megazyme.com es at dr hy o rb a C • s e t a r t s b u S e m y z n E • s e m y z n E • s t i K y a s s A Plant Cell Wall & Biofuels Product Guide 1 Megazyme Test Kits and Reagents Purity. Quality. Innovation. Barry V. McCleary, PhD, DScAgr Innovative test methods with exceptional technical support and customer service. The Megazyme Promise. Megazyme was founded in 1988 with the We demonstrate this through the services specific aim of developing and supplying we offer, above and beyond the products we innovative test kits and reagents for supply. We offer worldwide express delivery the cereals, food, feed and fermentation on all our shipments. In general, technical industries. There is a clear need for good, queries are answered within 48 hours. To validated methods for the measurement of make information immediately available to the polysaccharides and enzymes that affect our customers, we established a website in the quality of plant products from the farm 1994, and this is continually updated. Today, it gate to the final food. acts as the source of a wealth of information on Megazyme products, but also is the hub The commitment of Megazyme to “Setting of our commercial activities. It offers the New Standards in Test Technology” has been possibility to purchase and pay on-line, to continually recognised over the years, with view order history, to track shipments, and Megazyme and myself receiving a number many other features to support customer of business and scientific awards. -
Non-Homologous Isofunctional Enzymes: a Systematic Analysis Of
Omelchenko et al. Biology Direct 2010, 5:31 http://www.biology-direct.com/content/5/1/31 RESEARCH Open Access Non-homologousResearch isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution Marina V Omelchenko, Michael Y Galperin*, Yuri I Wolf and Eugene V Koonin Abstract Background: Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC) numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted) to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins. Results: We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE) that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. -
Cellulases: Characteristics, Sources, Production, and Applications
8 CELLULASES: CHARACTERISTICS, SOURCES, PRODUCTION, AND APPLICATIONS Xiao-Zhou Zhang and Yi-Heng Percival Zhang 8.1 INTRODUCTION lulases: (1) endoglucanases (EC 3.2.1.4), (2) exogluca- nases, including cellobiohydrolases (CBHs) (EC Cellulose is the most abundant renewable biological 3.2.1.91), and (3) β -glucosidase (BG) (EC 3.2.1.21). To resource and a low-cost energy source based on energy hydrolyze and metabolize insoluble cellulose, the micro- content ($3–4/GJ) ( Lynd et al., 2008 ; Zhang, 2009 ). The organisms must secrete the cellulases (possibly except production of bio-based products and bioenergy from BG) that are either free or cell-surface-bound. Cellu- less costly renewable lignocellulosic materials would lases are increasingly being used for a large variety of bring benefi ts to the local economy, environment, and industrial purposes—in the textile industry, pulp and national energy security ( Zhang, 2008 ). paper industry, and food industry, as well as an additive High costs of cellulases are one of the largest obsta- in detergents and improving digestibility of animal cles for commercialization of biomass biorefi neries feeds. Now cellulases account for a signifi cant share of because a large amount of cellulase is consumed for the world ’ s industrial enzyme market. The growing con- biomass saccharifi cation, for example, ∼ 100 g enzymes cerns about depletion of crude oil and the emissions of per gallon of cellulosic ethanol produced ( Zhang et al., greenhouse gases have motivated the production of bio- 2006b ; Zhu et al., 2009 ). In order to decrease cellulase ethanol from lignocellulose, especially through enzy- use, increase volumetric productivity, and reduce capital matic hydrolysis of lignocelluloses materials—sugar investment, consolidated bioprocessing ( CBP ) has been platform ( Bayer et al., 2007 ; Himmel et al., 1999 ; Zaldi- proposed by integrating cellulase production, cellulose var et al., 2001 ). -
United States Patent (19) 11 Patent Number: 5,981,835 Austin-Phillips Et Al
USOO598.1835A United States Patent (19) 11 Patent Number: 5,981,835 Austin-Phillips et al. (45) Date of Patent: Nov. 9, 1999 54) TRANSGENIC PLANTS AS AN Brown and Atanassov (1985), Role of genetic background in ALTERNATIVE SOURCE OF Somatic embryogenesis in Medicago. Plant Cell Tissue LIGNOCELLULOSC-DEGRADING Organ Culture 4:107-114. ENZYMES Carrer et al. (1993), Kanamycin resistance as a Selectable marker for plastid transformation in tobacco. Mol. Gen. 75 Inventors: Sandra Austin-Phillips; Richard R. Genet. 241:49-56. Burgess, both of Madison; Thomas L. Castillo et al. (1994), Rapid production of fertile transgenic German, Hollandale; Thomas plants of Rye. Bio/Technology 12:1366–1371. Ziegelhoffer, Madison, all of Wis. Comai et al. (1990), Novel and useful properties of a chimeric plant promoter combining CaMV 35S and MAS 73 Assignee: Wisconsin Alumni Research elements. Plant Mol. Biol. 15:373-381. Foundation, Madison, Wis. Coughlan, M.P. (1988), Staining Techniques for the Detec tion of the Individual Components of Cellulolytic Enzyme 21 Appl. No.: 08/883,495 Systems. Methods in Enzymology 160:135-144. de Castro Silva Filho et al. (1996), Mitochondrial and 22 Filed: Jun. 26, 1997 chloroplast targeting Sequences in tandem modify protein import specificity in plant organelles. Plant Mol. Biol. Related U.S. Application Data 30:769-78O. 60 Provisional application No. 60/028,718, Oct. 17, 1996. Divne et al. (1994), The three-dimensional crystal structure 51 Int. Cl. ............................. C12N 15/82; C12N 5/04; of the catalytic core of cellobiohydrolase I from Tricho AO1H 5/00 derma reesei. Science 265:524-528. -
Cells of Commelina Communis1 Received for Publication April 8, 1987 and in Revised Form June 13, 1987 NINA L
Plant Physiol. (1987) 85, 360-364 0032-0889/87/85/0360/05/$01.00/0 Localization of Carbohydrate Metabolizing Enzymes in Guard Cells of Commelina communis1 Received for publication April 8, 1987 and in revised form June 13, 1987 NINA L. ROBINSON2 AND JACK PREISS*3 Department ofBiochemistry and Biophysics, University ofCalifornia, Davis, California 95616 ABSTRACI leaves. The sucrose is either degraded in the apoplast or in the cytoplasm of the storage cell. Sucrose, or its degradation prod- The lliztion ofenzymes involved in the flow of carbon into and out ucts, can be further metabolized to the triose-P or 3-PGA level. of starch was determined in guard cells of Commelina communis. The These compounds may then move into the amyloplast via the guard cell chloroplasts were separated from the rest of the cellular triose-P/Pi translocator and are converted into starch. However, components by a modification of published microfuge methods. The at present, the presence of the triose-P/Pi translocator in amy- enzymes of interest were then assayed in the supernatant and chloroplast loplasts has not been demonstrated. Assuming that the triose-P/ fractions. The chloroplast yield averaged 75% with 10% cytoplasmic Pi translocator is present, the movement of carbon into starch contamination. The enzymes involved in starch biosynthesis, ADPglucose would be a reversal of the enzymic steps occurring in the cyto- pyrophosphorylase, starch synthase, and branching enzyme, are located plasm with the last several steps resulting in the direct incorpo- exclusively in the chloroplast fraction. The enzymes involved in starch ration of carbon into starch. -
Xylooligosaccharides Production, Quantification, and Characterization
19 Xylooligosaccharides Production, Quantification, and Characterization in Context of Lignocellulosic Biomass Pretreatment Qing Qing1, Hongjia Li2,3,4,Ã, Rajeev Kumar2,4 and Charles E. Wyman2,3,4 1 Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, China 2 Center for Environmental Research and Technology, University of California, Riverside, USA 3 Department of Chemical and Environmental Engineering, University of California, Riverside, USA 4 BioEnergy Science Center, Oak Ridge, USA 19.1 Introduction 19.1.1 Definition of Oligosaccharides Oligosaccharides, also termed sugar oligomers, refer to short-chain polymers of monosaccharide units con- nected by a and/or b glycosidic bonds. In structure, oligosaccharides represent a class of carbohydrates between polysaccharides and monosaccharides, but the range of degree of polymerization (DP, chain length) spanned by oligosaccharides has not been consistently defined. For example, the Medical Subject Headings (MeSH) database of the US National Library of Medicine defines oligosaccharides as carbohy- drates consisting of 2–10 monosaccharide units; in other literature, sugar polymers with DPs of up to 30–40 have been included as oligosaccharides [1–3]. ÃPresent address: DuPont Industrial Biosciences, Palo Alto, USA Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, First Edition. Edited by Charles E. Wyman. Ó 2013 John Wiley & Sons, Ltd. Published 2013 by John Wiley & Sons, Ltd. 392 Aqueous Pretreatment of Plant Biomass for -
How Liquorilactobacillus Hordei TMW 1.1822 Changes Its Behavior in the Presence of Sucrose in Comparison to Glucose
foods Article Living the Sweet Life: How Liquorilactobacillus hordei TMW 1.1822 Changes Its Behavior in the Presence of Sucrose in Comparison to Glucose Julia Bechtner 1 , Christina Ludwig 2, Michael Kiening 3, Frank Jakob 1 and Rudi F. Vogel 1,* 1 Lehrstuhl für Technische Mikrobiologie, Technische Universität München (TUM), 85354 Freising, Germany; [email protected] (J.B.); [email protected] (F.J.) 2 Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), 85354 Freising, Germany; [email protected] 3 Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität München (TUM), 85354 Freising, Germany; [email protected] * Correspondence: [email protected] Received: 2 August 2020; Accepted: 17 August 2020; Published: 21 August 2020 Abstract: Liquorilactobacillus (L.) hordei (formerly Lactobacillus hordei) is one of the dominating lactic acid bacteria within the water kefir consortium, being highly adapted to survive in this environment, while producing high molecular weight dextrans from sucrose. In this work, we extensively studied the physiological response of L. hordei TMW 1.1822 to sucrose compared to glucose, applying label-free, quantitative proteomics of cell lysates and exoproteomes. This revealed the differential expression of 53 proteins within cellular proteomes, mostly associated with carbohydrate uptake and metabolism. Supported by growth experiments, this suggests that L. hordei TMW 1.1822 favors fructose over other sugars. The dextransucrase was expressed irrespectively of the present carbon source, while it was significantly more released in the presence of sucrose (log2FC = 3.09), being among the most abundant proteins within exoproteomes of sucrose-treated cells. Still, L. hordei TMW 1.1822 expressed other sucrose active enzymes, predictively competing with the dextransucrase reaction. -
Identification and Characterization of an Endo-Glucanase Secreted From
Pang et al. BMC Biotechnology (2019) 19:63 https://doi.org/10.1186/s12896-019-0556-0 RESEARCH ARTICLE Open Access Identification and characterization of an Endo-glucanase secreted from cellulolytic Escherichia coli ZH-4 Jian Pang1,3, Junshu Wang2*, Zhanying Liu1,3*, Qiancheng Zhang1 and Qingsheng Qi2 Abstract Background: In the previous study, the cellulolytic Escherichia coli ZH-4 isolated from bovine rumen was found to show extracellular cellulase activity and could degrade cellulose in the culture. The goal of this work was to identify and characterize the secreted cellulase of E. coli ZH-4. It will be helpful to re-understand E. coli and extend its application in industry. Results: A secreted cellulase was confirmed to be endo-glucanase BcsZ which was encoded by bcsZ gene and located in the cellulose synthase operon bcsABZC in cellulolytic E. coli ZH-4 by western blotting. Characterization of BcsZ indicated that a broad range of pH and temperature tolerance with optima at pH 6.0 and 50 °C, respectively. The apparent Michaelis–Menten constant (Km) and maximal reaction rate (Vmax) for BcsZ were 8.86 mg/mL and 0.3 μM/ min·mg, respectively. Enzyme activity of BcsZ was enhanced by Mg2+ and inhibited by Zn2+,Cu2+ and Fe3+. BcsZ could hydrolyze carboxymethylcellulose (CMC) to produce cello-oligosaccharides, cellotriose, cellobiose and glucose. Conclusions: It is confirmed that extracellular cellulolytic capability of E. coli ZH-4 was attributed to BcsZ, which explained why E. coli ZH-4 can grow on cellulose. The endo-glucanase BcsZ from E. coli-ZH4 has some new characteristics which will extend the understanding of endo-glucanase. -
Microbial Beta Glucosidase Enzymes: Recent Advances in Biomass Conversation for Biofuels Application
biomolecules Review Microbial Beta Glucosidase Enzymes: Recent Advances in Biomass Conversation for Biofuels Application 1, , 2 3 1 4, Neha Srivastava * y, Rishabh Rathour , Sonam Jha , Karan Pandey , Manish Srivastava y, Vijay Kumar Thakur 5,* , Rakesh Singh Sengar 6, Vijai K. Gupta 7,* , Pranab Behari Mazumder 8, Ahamad Faiz Khan 2 and Pradeep Kumar Mishra 1,* 1 Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India; [email protected] 2 Department of Bioengineering, Integral University, Lucknow 226026, India; [email protected] (R.R.); [email protected] (A.F.K.) 3 Department of Botany, Banaras Hindu University, Varanasi 221005, India; [email protected] 4 Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India; [email protected] 5 Enhanced Composites and Structures Center, School of Aerospace, Transport and Manufacturing, Cranfield University, Bedfordshire MK43 0AL, UK 6 Department of Agriculture Biotechnology, College of Agriculture, Sardar Vallabhbhai Patel, University of Agriculture and Technology, Meerut 250110, U.P., India; [email protected] 7 Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia 8 Department of Biotechnology, Assam University, Silchar 788011, India; [email protected] * Correspondence: [email protected] (N.S.); vijay.Kumar@cranfield.ac.uk (V.K.T.); [email protected] (V.K.G.); [email protected] (P.K.M.); Tel.: +372-567-11014 (V.K.G.); Fax: +372-620-4401 (V.K.G.) These authors have equal contribution. y Received: 29 March 2019; Accepted: 28 May 2019; Published: 6 June 2019 Abstract: The biomass to biofuels production process is green, sustainable, and an advanced technique to resolve the current environmental issues generated from fossil fuels. -
A Xyloglucan-Specific Endo-Β-1,4-Glucanase from Aspergillus Aculeatus: Expression Cloning in Yeast, Purification and Characterization of the Recombinant Enzyme
Glycobiology vol. 9 no. 1 pp. 93–100, 1999 A xyloglucan-specific endo-β-1,4-glucanase from Aspergillus aculeatus: expression cloning in yeast, purification and characterization of the recombinant enzyme Markus Pauly, Lene N.Andersen1, Sakari Kauppinen1, may also modulate the action of a XG endotransglycosylase Lene V.Kofod1, William S.York2, Peter Albersheim and (XET), a cell wall–associated enzyme that may play a role in the Alan Darvill elongation of plant cell walls (Fry et al., 1992). Therefore, XG Complex Carbohydrate Research Center and Department of Biochemistry and metabolism might play an important role in wall loosening and Molecular Biology, University of Georgia, 220 Riverbend Road, Athens, consequent cell expansion. GA 30602–4712, USA and 1Novo Nordisk A/S, Novo Alle, The fine structural features of XG reflect its metabolic history, DK-2880 Bagsværd, Denmark and so analysis of the oligosaccharide subunit composition of XGs Received on May 4, 1998; revised on June 2, 1998; accepted on June 7, 1998 isolated from plant tissues under varying physiological conditions can reveal a correlation between cell expansion and XG metabolism 2To whom correspondence should be addressed (Guillen et al., 1995). XG is often solubilized by treating cell walls A full-length c-DNA encoding a xyloglucan-specific with strong alkali (e.g., 4 M KOH), perhaps by disruption of the endo-β-1,4-glucanase (XEG) has been isolated from the hydrogen bonds between XG and cellulose (Hayashi et al., 1987). filamentous fungus Aspergillus aculeatus by expression However, this harsh chemical treatment of the wall destroys some cloning in yeast.