DOCSLIB.ORG

Download Author Version (PDF)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Download Author Version (PDF) Molecular BioSystems Accepted Manuscript This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. We will replace this Accepted Manuscript with the edited and formatted Advance Article as soon as it is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/molecularbiosystems Page 1 of 30 Molecular BioSystems 1 Depiction of Carbohydrate-Active Enzymes Diversity in Caldicellulosiruptor sp. F32 at 2 Genome Level Reveals Insights into Distinct Polysaccharides Degradation Feature 3 4 Dong-Dong Meng1, Yu Ying1,2, Kun-Di Zhang1, Ming Lu1, and Fu-Li Li1* Manuscript 5 6 1Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao 7 Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 8 266101, China 2 9 Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Accepted 10 266071, China 11 12 *Corresponding author: Fu-Li Li, Qingdao Institute of Bioenergy and Bioprocess Technology, 13 Chinese Academy of Sciences, Qingdao, 266101, China. Tel.: 86-532-80662655. Fax: 14 86-532-80662778. E-mail: [email protected] 15 BioSystems 1 Molecular Molecular BioSystems Page 2 of 30 16 Abstract 17 Thermophilic bacterium Caldicellulosiruptor sp. F32 can utilize cellulose-, 18 hemicellulose-containing biomass, including unpretreated wheat straw. We have conducted a 19 bioinformatics analysis of the carbohydrate-active enzyme (CAZyme) in the genome of 20 Caldicellulosiruptor sp. F32, which reveals a broad substrate range of the strain. Among 2285 Manuscript 21 predicted open reading frames (ORFs), 73 (3.2%) CAZyme encoding genes, including 44 22 glycoside hydrolases (GHs) distributing in 22 GH families, 6 carbohydrate esterases (CEs), 3 23 polysaccharide lyases (PLs), 21 glycosyl transferases (GTs), and 25 carbohydrate-binding 24 modules (CBMs) were found. An in-depth bioinformatics analysis of CAZyme families that 25 target cellulose, hemicellulose, chitin, pectin, starch, and β-1,3-1,4-glucan degradation were Accepted 26 performed to highlight specialized polysaccharides degrading abilities of strain F32. A great 27 number of orthologous multimodular CAZymes of Caldicellulosiruptor sp. F32 were found in 28 other strains of genus Caldicellulosiruptor. While, a portion of the CAZymes of 29 Caldicellulosiruptor sp. F32 showed sequence identity with proteins from strains of genus 30 Clostridium. A thermostable β-glucosidase BlgA synergistically facilitated enzymatic 31 degradation of Avicel by endo-1,4-β-glucanase CelB, which indicated that synchronous action of BioSystems 32 synergism between CAZymes enhanced the lignocellulose degradation of Caldicellulosiruptor sp. 33 F32. 34 35 Keywords: CAZymes; Glycoside hydrolase; Lignocellulose; Synergism; Caldicellulosiruptor 36 2 Molecular Page 3 of 30 Molecular BioSystems 37 Introduction 38 Thermophilic bacteria of genus Caldicellulosiruptor (Topt 65–78 °C) are robust and efficient 39 carbohydrate degrading microorganisms, which secrete a series of carbohydrate active enzymes 40 (CAZymes) to deconstruct lignocellulosic biomass1. Gram-positive Caldicellulosiruptor spp. 41 have been isolated from a wide variety of ecological niches. Most of the species can metabolize Manuscript 42 an extensive monosaccharides, oligosaccharides, and polysaccharides, including crystalline 43 cellulose, xylan, and switchgrass2. Furthermore, since no carbon catabolite repression (CCR) 44 system exists in C. saccharolyticus, this strain has been shown to be able to ferment C5 and C6 45 sugars simultaneously, which was a highly desirable feature for lignocellulose conversion3, 4. All 46 isolates are given a diverse set of cell wall degrading enzymes (CWDEs) as an excellent Accepted 47 CAZymes reservoir for carbohydrate degradation, which are potential consolidated 48 bioprocessing (CBP) platforms for biomass-to-biofuel conversion. Cellulolytic enzymes systems 49 can be divided into two main categories, namely cellulosomal and noncellulosomal. Genus 50 Caldicellulosiruptor adopts an intermediate strategy, secreting many free multi-modular 51 cellulases containing multiple binding and catalytic domains5. 52 Blumer-Schuette et al. have examined the CAZymes of eight numbers of this genus. Each BioSystems 53 strain contains a significant number of glycoside hydrolases (GHs, 37~77), carbohydrate binding 54 modules (CBMs, 15~28), polysaccharide lyases (PLs, 1~4), carbohydrate esterases (CEs, 4~9), 55 and glycosyl transferases (GTs, 27~35)2, which comprise 1%~3% of the genome. Comparison 56 analysis within the genus from genome level indicates 106 GHs distributing in 43 GH families 57 constitute the Caldicellulosiruptor pangenome, while 26 GHs from 17 families are conserved in 3 Molecular Molecular BioSystems Page 4 of 30 58 the core genome2. Though more than half of the lignocellulose degradation related proteins are 59 shared between all Caldicellulosiruptor species, genomic and proteomic studies in one individual 60 species are needed to distinguish the difference of carbohydrate utilization within the genus6. As 61 an efficient lignocellulolytic bacterium toward unpretreated plant biomass, analysis of CAZyme 62 families and its architecture composition at genome level is helpful to elucidate the ability of Manuscript 63 Caldicellulosiruptor species for deconstruction of plant polysaccharides. 64 Caldicellulosiruptor sp. F32 is an extremely thermophilic anaerobic bacterium, which was 65 isolated from biocompost with optimal growth temperature at 75 °C7. Compared with the type 66 stain C. saccharolyticus DSM 8903, Caldicellulosiruptor sp. F32 grew better on unpretreated 67 wheat straw, exhibited higher endoglucanase and xylanase activities in the secretome8. Three Accepted 68 CAZy enzymes, GH11 xylanase XynA (GenBank accession number JX030400), GH10 xylanase 69 XynB (GenBank accession number JX030401)9, and GH5 lichenase F32EG5 (GenBank 70 accession number KC958563, unpublished) have been characterized in detail. Further elucidation 71 of the abundant CAZymes is thus essential to understand the complexity process of the 72 lignocellulose deconstruction. This report focused on the CAZymes identification of strain F32 73 and provided a wealth of information to generate a comprehensive analysis of CWDEs in the BioSystems 74 host. Sequence and module annotation have been applied to predict functions of each CAZyme 75 proteins. Moreover, synergism between two cellulose-degrading enzymes was investigated. 76 Briefly, this will provide a better understanding of the plant-biomass degradation mechanisms of 77 the genus Caldicellulosiruptor. 78 4 Molecular Page 5 of 30 Molecular BioSystems 79 Materials and method 80 Genomic DNA isolation and genome sequencing 81 Caldicellulosiruptor sp. F32 (CGMCC 1.5183, China General Microbiological Collection 82 Center, Beijing, China) was cultured at 75 °C in an anaerobic jar containing modified GS-2 83 medium7. Genomic DNA was isolated10 from Caldicellulosiruptor sp. F32 and was sequenced by Manuscript 84 a standard shotgun strategy using GS FLX-454 pyrosequencing technology (Roche, Basel, 85 Switzerland). The numerous reads were assembled by using the 454 Newbler assembler software 86 (Roche) into hundreds of contigs, which were re-sorted subsequently to predict gene functions 87 using Glimmer11, GeneMark12, and Zcurve13. The genes were annotated through the National 88 Center for Biotechnology Information (NCBI) nr database14 and KEGG database15. Accepted 89 CAZymes annotation 90 All protein-encoding open reading frames (ORFs) from the Caldicellulosiruptor sp. F32 91 genome generated through nr and KEGG databases annotation, were further refined and screened 92 for carbohydrate-active modules using Carbohydrate-active enzyme ANnotatio (dbCAN, 93 http://csbl.bmb.uga.edu/dbCAN/index.php)16. To eliminate proteins identified by dbCAN but 94 those were not really CAZymes, all proteins were individually examined using NCBI’s BioSystems 95 Conserved Domain Database (CDD) (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi)17 96 and Pfam (http://pfam.sanger.ac.uk/)18. These data sources were combined to assert the function 97 of each predicted proteins. When a gene appeared to be truncated and the missing sequence data 98 couldn’t be found within all the supercontig, the orthologous coding region in other 99 Caldicellulosiruptor isolates were used to modify the gene sequence from Caldicellulosiruptor 5 Molecular Molecular BioSystems Page 6 of 30 100 sp. F32 genome. Further annotation of selected proteins included protein similarities and 101 identities determination19, molecular size and isoelectric point prediction20, and signal peptide 102 prediction (SignalP v4.1)21. 103 Cloning, expression, and purification of Caldicellulosiruptor
Load more

Recommended publications
  • Agency Response Letter GRAS Notice No. GRN 000675
    . Janet Oesterling Novozymes North America, Inc. 77 Perry Chapel Church Road Franklinton, NC 27525 Re: GRAS Notice No. GRN 000675 Dear Ms. Oesterling: The Food and Drug Administration (FDA, we) completed our evaluation of GRN 000675. We received the notice, dated October 10, 2016, that you submitted in accordance with the agency’s proposed regulation, proposed 21 CFR 170.36 (62 FR 18938; April 17, 1997; Substances Generally Recognized as Safe (GRAS); the GRAS proposal) on July 17, 2016, and filed it on October 14, 2016. We received amendments containing clarifying information on February, 22, 2017 and March 09, 2017. FDA published the GRAS final rule on August 17, 2016 (81 FR 54960), with an effective date of October 17, 2016. As GRN 000675 was pending on the effective date of the GRAS final rule, we requested some additional information consistent with the format and requirements of the final rule. We received an amendment responding to this request on October 24, 2016. The subject of the notice is xylanase enzyme preparation produced by Trichoderma reesei carrying a xylanase gene from Talaromyces leycettanus (xylanase enzyme preparation). The notice informs us of the view of Novozymes North America, Inc. (Novozymes) that xylanase enzyme preparation is GRAS, through scientific procedures, for use as an enzyme at levels up to 48.33 mg Total Organic Solids (TOS) per kg raw material in brewing, cereal beverage processing, baking, and processing of cereal grains such as corn, wheat, barley, and oats. Commercial enzyme preparations that are used in food processing typically contain an enzyme component that catalyzes the chemical reaction as well as substances used as stabilizers, preservatives, or diluents.
    [Show full text]
  • 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 ).
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Novel Xylan Degrading Enzymes from Polysaccharide Utilizing Loci of Prevotella Copri DSM18205
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.419226; this version posted December 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Novel xylan degrading enzymes from polysaccharide utilizing loci of Prevotella copri DSM18205 Javier A. Linares-Pastén1*, Johan Sebastian Hero2, José Horacio Pisa2, Cristina Teixeira1, Margareta Nyman3, Patrick Adlercreutz1, M. Alejandra Martinez2,4, Eva Nordberg Karlsson1** 1Biotechnology, Dept of Chemistry, Lund University, P.O.Box 124, 221 00 Lund, Sweden. 2Planta Piloto de Procesos Industriales Microbiológicos PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, San Miguel de Tucumán, Argentina. 3 Dept Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden. 4Facultad de Ciencias Exactas y Tecnología, UNT. Av. Independencia 1800, San Miguel de Tucumán, 4000, Argentina. Corresponding authors: *e-mail: [email protected] ** e-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.419226; this version posted December 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Prevotella copri DSM18205 is a bacterium, classified under Bacteroidetes that can be found in the human gastrointestinal tract (GIT). The role of P. copri in the GIT is unclear, and elevated numbers of the microbe have been reported both in dietary fiber- induced improvement in glucose metabolism but also in conjunction with certain inflammatory conditions.
    [Show full text]
  • Exogenous Enzymes As Zootechnical Additives in Animal Feed: a Review
    catalysts Review Exogenous Enzymes as Zootechnical Additives in Animal Feed: A Review Brianda Susana Velázquez-De Lucio 1, Edna María Hernández-Domínguez 1, Matilde Villa-García 1, Gerardo Díaz-Godínez 2, Virginia Mandujano-Gonzalez 3, Bethsua Mendoza-Mendoza 4 and Jorge Álvarez-Cervantes 1,* 1 Cuerpo Académico Manejo de Sistemas Agrobiotecnológicos Sustentables, Posgrado Biotecnología, Universidad Politécnica de Pachuca, Zempoala 43830, Hidalgo, Mexico; [email protected] (B.S.V.-D.L.); [email protected] (E.M.H.-D.); [email protected] (M.V.-G.) 2 Centro de Investigación en Ciencias Biológicas, Laboratorio de Biotecnología, Universidad Autónoma de Tlaxcala, Tlaxcala 90000, Tlaxcala, Mexico; [email protected] 3 Ingeniería en Biotecnología, Laboratorio Biotecnología, Universidad Tecnológica de Corregidora, Santiago de Querétaro 76900, Querétaro, Mexico; [email protected] 4 Instituto Tecnológico Superior del Oriente del Estado de Hidalgo, Apan 43900, Hidalgo, Mexico; [email protected] * Correspondence: [email protected]; Tel.: +52-771-5477510 Abstract: Enzymes are widely used in the food industry. Their use as a supplement to the raw Citation: Velázquez-De Lucio, B.S.; material for animal feed is a current research topic. Although there are several studies on the Hernández-Domínguez, E.M.; application of enzyme additives in the animal feed industry, it is necessary to search for new Villa-García, M.; Díaz-Godínez, G.; enzymes, as well as to utilize bioinformatics tools for the design of specific enzymes that work in Mandujano-Gonzalez, V.; certain environmental conditions and substrates. This will allow the improvement of the productive Mendoza-Mendoza, B.; Álvarez-Cervantes, J.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Mapping the Transglycosylation Relevant Sites of Cold-Adapted -D
    International Journal of Molecular Sciences Article Mapping the Transglycosylation Relevant Sites of Cold-Adapted β-d-Galactosidase from Arthrobacter sp. 32cB Maria Rutkiewicz 1,2,* , Marta Wanarska 3 and Anna Bujacz 1 1 Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; [email protected] 2 Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany 3 Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland; [email protected] * Correspondence: [email protected] Received: 30 June 2020; Accepted: 24 July 2020; Published: 28 July 2020 Abstract: β-Galactosidase from Arthrobacter sp. 32cB (ArthβDG) is a cold-adapted enzyme able to catalyze hydrolysis of β-d-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of ArthβDG: D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to shed light onto the structural basis of the transglycosylation reaction. The catalytic assays proved loss of function mutation E517 into glutamine and a significant drop of activity for mutation of D207 into alanine. Solving crystal structures of two new mutants, and new complex structures of previously presented mutant E441Q enables description of introduced changes within active site of enzyme and determining the importance of mutated residues for active site size and character.
    [Show full text]
  • Synthesis of Three Advanced Biofuels from Ionic Liquid-Pretreated Switchgrass Using Engineered Escherichia Coli
    Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli Gregory Bokinskya,b, Pamela P. Peralta-Yahyaa,b, Anthe Georgea,c, Bradley M. Holmesa,c, Eric J. Steena,d, Jeffrey Dietricha,d, Taek Soon Leea,e, Danielle Tullman-Erceka,f, Christopher A. Voigtg, Blake A. Simmonsa,c, and Jay D. Keaslinga,b,d,e,f,1 aJoint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA 94608; bQB3 Institute, University of California, San Francisco, CA 94158; cSandia National Laboratories, P.O. Box 969, Livermore, CA 94551; dDepartment of Bioengineering, and ePhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; fDepartment of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720; and gDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited by Alexis T. Bell, University of California, Berkeley, CA, and approved November 2, 2011 (received for review May 2, 2011) One approach to reducing the costs of advanced biofuel production Unfortunately, several challenges must be overcome before from cellulosic biomass is to engineer a single microorganism to lignocellulose can be considered an economically competitive both digest plant biomass and produce hydrocarbons that have feedstock for biofuel production. One of the more significant chal- the properties of petrochemical fuels. Such an organism would lenges is the need for large quantities of glycoside hydrolase (GH) require pathways for hydrocarbon
    [Show full text]
  • Enzyme Applications in Pulp and Paper Industry
    Enzyme Applications in Pulp and Paper: An Introduction to Applications Dr. Richard Venditti Associate Professor - Director of Graduate Programs Department of Wood and Paper Science Biltmore Hall Room 1204 Raleigh NC 27695-8005 Tel. (919) 515-6185 Fax. (919) 515-6302 Email: [email protected] Slides courtesy of Phil Hoekstra. Endo-Beta 1,4 Xylanase Enzymes • Are proteins that catalyze chemical reactions • Biological cells need enzymes to perform needed functions • The starting molecules that enzymes process are called substrates and these are converted to products Endo-Beta 1,4 Xylanase Cellulase enzyme which acts on cellulose substrate to make product of glucose. Endo-Beta 1,4 Xylanase Enzymes • Are extremely selective for specific substrates • Activity affected by inhibitors, pH, temperature, concentration of substrate • Commercial enzyme products are typically mixtures of different enzymes, the enzymes often complement the activity of one another Endo-Beta 1,4 Xylanase Types of Enzymes in Pulp and Paper and Respective Substrates • Amylase --- starch • Cellulase --- cellulose fibers • Protease --- proteins • Hemicellulases(Xylanase) ---hemicellulose • Lipase --- glycerol backbone, pitch • Esterase --- esters, stickies • Pectinase --- pectins Endo-Beta 1,4 Xylanase Enzyme Applications in Pulp and Paper • Treat starches for paper applications • Enhanced bleaching • Treatment for pitch • Enhanced deinking • Treatment for stickies in paper recycling • Removal of fines • Reduce refining energy • Cleans white water systems • Improve
    [Show full text]