Comparing Ligninolytic Capabilities of Bacterial and Fungal Dye-Decolorizing Peroxidases and Class-II Peroxidase-Catalases
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Deconstruction of Lignin: from Enzymes to Microorganisms
molecules Review Deconstruction of Lignin: From Enzymes to Microorganisms Jéssica P. Silva 1, Alonso R. P. Ticona 1 , Pedro R. V. Hamann 1, Betania F. Quirino 2 and Eliane F. Noronha 1,* 1 Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; [email protected] (J.P.S.); [email protected] (A.R.P.T.); [email protected] (P.R.V.H.) 2 Genetics and Biotechnology Laboratory, Embrapa-Agroenergy, 70770-901 Brasília, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-61-3307-2152 Abstract: Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses. -
Oxidative Degradation of Non-Phenolic Lignin During Lipid Peroxidation by Fungal Manganese Peroxidase
FEBS Letters 354 (1994) 297-300 FEBS 14759 Oxidative degradation of non-phenolic lignin during lipid peroxidation by fungal manganese peroxidase Wuli Bao, Yaichi Fukushima, Kenneth A. Jensen Jr., Mark A. Moen, Kenneth E. Hammel* USDA Forest Products Laboratory, Madison, WI 53705, USA Received 3 October 1994 Abstract A non-phenolic lignin model dimer, 1-(4-ethoxy-3-methoxyphenyl)-2-phenoxypropane-l ,3-diol, was oxidized by a lipid peroxidation system that consisted of a fungal manganese peroxidase, Mn(II), and unsaturated fatty acid esters. The reaction products included 1-(4-ethoxy-3- methoxyphenyl)-1-oxo-2-phenoxy-3-hydroxypropane and 1-(4-ethoxy-3-methoxyphenyl)- 1-oxo-3-hydroxypropane, indicating that substrate oxida- tion occurred via benzylic hydrogen abstraction. The peroxidation system depolymerized both exhaustively methylated (non-phenolic) and unmeth- ylated (phenolic) synthetic lignins efficiently. It may therefore enable white-rot fungi to accomplish the initial delignification of wood. Key words: Manganese peroxidase; Lipid peroxidation; Ligninolysis; Non-phenolic lignin; White-rot fungus 1. Introduction 2. Materials and methods White-rot fungi have evolved unique ligninolytic mecha- 2.1. Reagents l-(4-Ethoxy-3-methoxyphenyl)-2-phenoxypropane-l,3-diol (I) [12] nisms, which enable them to play an essential role in terrestrial 1-(4-ethoxy-3-methoxyphenyl)-l-oxo-2-phenoxy-3-hydroxypropane ecosystems by degrading and recycling lignified biomass. The (II) [13], and l-(4-ethoxy-3-methoxyphenyl)-l-oxo-3-hydroxypropane chemical recalcitrance, random structure, and large size of lig- (III) [14] were prepared by the indicated methods.I labeled with 14C at Cl (0.066 mCi· mmol-1) was prepared in the same manner as the unla- nin require that these mechanisms be oxidative, non-specific, 14 beled compound, using [1- C]acetic acid as the labeled precursor. -
SUPPLEMENTARY DATA Supplementary Figure 1. The
SUPPLEMENTARY DATA Supplementary Figure 1. The results of Sirt1 activation in primary cultured TG cells using adenoviral system. GFP expression served as the control (n = 4 per group). Supplementary Figure 2. Two different Sirt1 activators, SRT1720 (0.5 µM or 1 µM ) and RSV (1µM or 10µM), induced the upregulation of Sirt1 in the primary cultured TG cells (n = 4 per group). ©2016 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db15-1283/-/DC1 SUPPLEMENTARY DATA Supplementary Table 1. Primers used in qPCR Gene Name Primer Sequences Product Size (bp) Sirt1 F: tgccatcatgaagccagaga 241 (NM_001159589) R: aacatcgcagtctccaagga NOX4 F: tgtgcctttattgtgcggag 172 (NM_001285833.1) R: gctgatacactggggcaatg Supplementary Table 2. Antibodies used in Western blot or Immunofluorescence Antibody Company Cat. No Isotype Dilution Sirt1 Santa Cruz * sc-15404 Rabbit IgG 1/200 NF200 Sigma** N5389 Mouse IgG 1/500 Tubulin R&D# MAB1195 Mouse IgG 1/500 NOX4 Abcam† Ab133303 Rabbit IgG 1/500 NOX2 Abcam Ab129068 Rabbit IgG 1/500 phospho-AKT CST‡ #4060 Rabbit IgG 1/500 EGFR CST #4267 Rabbit IgG 1/500 Ki67 Santa Cruz sc-7846 Goat IgG 1/500 * Santa Cruz Biotechnology, Santa Cruz, CA, USA ** Sigma aldrich, Shanghai, China # R&D Systems Inc, Minneapolis, MN, USA † Abcam, Inc., Cambridge, MA, USA ‡ Cell Signaling Technology, Inc., Danvers, MA, USA ©2016 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db15-1283/-/DC1 SUPPLEMENTARY DATA Supplementary -
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PEER-REVIEWED ARTICLE bioresources.com HYPERPRODUCTIVITY OF EXTRACELLULAR ENZYMES FROM INDIGENOUS WHITE ROT FUNGI (P. chrysosporium IBL-03) BY UTILIZING AGRO-WASTES Muhammad Asgher, Nadeem Ahmed, and Hafiz Muhammad Nasir Iqbal* An indigenous locally isolated white rot fungal strain Phanerochaete chrysosporium IBL-03 was investigated for the hyper-production of ligninolytic enzymes from different agro-industrial wastes including wheat straw, rice straw, banana stalks, corncobs, corn stover, and sugarcane bagasse as substrate material in still culture fermentation technique. Screening experiments were performed at 30oC from 1 to 10 days and maximum enzyme activities were recorded after the 5th day of incubation on banana stalk. P. chrysosporium IBL-03 produced highest activities of lignin peroxidase (LiP) and manganese peroxidase (MnP) but no laccase activity was detected in any fermented culture media. Production of ligninolytic enzymes was substantially enhanced through the optimization process. When banana stalk at 66.6 % moisture level and pH 4.5 was inoculated with 5mL spore suspension of P. chrysosporium IBL-03 at 35oC in the presence of molasses (1%) as carbon source, ammonium sulfate (0.2%) as nitrogen supplement, (1%) Tween-80 (0.3 mL) as surfactant and mediators (MnSO4 and veratryl alcohol) enhanced the LiP and MnP production up to 1040 and 965 (U/mL), respectively. Keywords: Phanerochaete chrysosporium IBL-03; Extracellular enzymes; Agro-wastes; SSF; Optimization Contact information: Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad Pakistan; * Corresponding Author: Telephone# +92-307-6715243 E-mail: [email protected] INTRODUCTION White rot fungi (WRF) are among the most robust micro-organisms, having the ability to degrade the major components of lignocellulosic sources, cellulose, hemicelluloses, and lignin as available hydrolyzable nutrients efficiently through their nonspecific and non stereo-selective extracellular enzyme system (Papinutti and Forchiassin 2007; Ruhl et al. -
Kinetic Approaches to Measuring Peroxiredoxin Reactivity
Mol. Cells 2016; 39(1): 26-30 http://dx.doi.org/10.14348/molcells.2016.2325 Molecules and Cells http://molcells.org Established in 1990 Kinetic Approaches to Measuring Peroxiredoxin Reactivity Christine C. Winterbourn*, and Alexander V. Peskin Peroxiredoxins are ubiquitous thiol proteins that catalyse demonstrated surprisingly low reactivity with thiol reagents such the breakdown of peroxides and regulate redox activity in as iodoacetamide and other oxidants such as chloramines the cell. Kinetic analysis of their reactions is required in (Peskin et al., 2007) and it is clear that the low pKa of the active order to identify substrate preferences, to understand how site thiol is insufficient to confer the high peroxide reactivity. In molecular structure affects activity and to establish their fact, typical low molecular weight and protein thiolates react -1 -1 physiological functions. Various approaches can be taken, with H2O2 with a rate constant of 20 M s whereas values of including the measurement of rates of individual steps in Prxs are 105-106 fold higher (Winterbourn and Hampton, 2008). the reaction pathway by stopped flow or competitive kinet- An elegant series of structural and mutational studies (Hall et al., ics, classical enzymatic analysis and measurement of pe- 2010; Nakamura et al., 2010; Nagy et al., 2011) have shown roxidase activity. Each methodology has its strengths and that to get sufficient rate enhancement, it is necessary to acti- they can often give complementary information. However, vate the peroxide. As discussed in detail elsewhere (Hall et al., it is important to understand the experimental conditions 2010; 2011), this involves formation of a transition state in of the assay so as to interpret correctly what parameter is which hydrogen bonding of the peroxide to conserved Arg and being measured. -
Prokaryotic Origins of the Non-Animal Peroxidase Superfamily and Organelle-Mediated Transmission to Eukaryotes
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Genomics 89 (2007) 567–579 www.elsevier.com/locate/ygeno Prokaryotic origins of the non-animal peroxidase superfamily and organelle-mediated transmission to eukaryotes Filippo Passardi a, Nenad Bakalovic a, Felipe Karam Teixeira b, Marcia Margis-Pinheiro b,c, ⁎ Claude Penel a, Christophe Dunand a, a Laboratory of Plant Physiology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland b Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil c Department of Genetics, Federal University of Rio Grande do Sul, Rio Grande do Sul, Brazil Received 16 June 2006; accepted 18 January 2007 Available online 13 March 2007 Abstract Members of the superfamily of plant, fungal, and bacterial peroxidases are known to be present in a wide variety of living organisms. Extensive searching within sequencing projects identified organisms containing sequences of this superfamily. Class I peroxidases, cytochrome c peroxidase (CcP), ascorbate peroxidase (APx), and catalase peroxidase (CP), are known to be present in bacteria, fungi, and plants, but have now been found in various protists. CcP sequences were detected in most mitochondria-possessing organisms except for green plants, which possess only ascorbate peroxidases. APx sequences had previously been observed only in green plants but were also found in chloroplastic protists, which acquired chloroplasts by secondary endosymbiosis. CP sequences that are known to be present in prokaryotes and in Ascomycetes were also detected in some Basidiomycetes and occasionally in some protists. -
Lactoperoxidase Antibacterial System: Natural Occurrence, Biological Functions and Practical Applications
724 Journal of Food Protection, Vol. 47. No. 9, Pages 724-732 (September 1984) Copyright®, International Association of Milk, Food, and Environmental Sanitarians Lactoperoxidase Antibacterial System: Natural Occurrence, Biological Functions and Practical Applications BRUNO REITER1 and GORAN HARNULV2* Downloaded from http://meridian.allenpress.com/jfp/article-pdf/47/9/724/1650811/0362-028x-47_9_724.pdf by guest on 29 September 2021 National Institute for Research in Dairying, Shinfield, Reading, RG2 9AT, England and Alfa-Laval Agri International AS, P.O. Box 39, S-I47 00 Tumba, Sweden (Received for publication January 30, 1984) ABSTRACT (37,80). The various biological functions of the LP sys tem, which have now been established, will be discussed In the present review dealing with the antibacterial lac below. toperoxidase (LP) system, it is shown that the two reactants In recent years, much work has been devoted to practi thiocyanate (SCN~) and hydrogen peroxide (H202) as well as cal applications of the LP system. The effect against oral the catalytic enzyme lactoperoxidase (LP) are widely distributed streptococci (5,19,33,101,105,107) has led to the de in nature and that evidence for the activity of the LP system velopment and marketing of a toothpaste containing nec in animals, including man, is accumulating. The in vitro effects on bacterial and animal cells are discussed and the unique ac essary ingredients to activate the LP system. Promising tion of the LP system on the bacterial cytoplasmic membrane results have also been obtained when including activating is pointed out. Some practical applications are also presented, components in the feed to calves (81,83,86) with the aim with particular emphses on the possibility of utilizing the LP of potentiating the LP system in the intestinal tract. -
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PEER-REVIEWED REVIEW ARTICLE bioresources.com BIOLOGICAL PRETREATMENT OF LIGNOCELLULOSES WITH WHITE-ROT FUNGI AND ITS APPLICATIONS: A REVIEW a,b c, d Isroi, Ria Millati, * Siti Syamsiah, Claes Niklasson,b Muhammad Nur Cahyanto,c f Knut Lundquist,e and Mohammad J. Taherzadeh Lignocellulosic carbohydrates, i.e. cellulose and hemicellulose, have abundant potential as feedstock for production of biofuels and chemicals. However, these carbohydrates are generally infiltrated by lignin. Breakdown of the lignin barrier will alter lignocelluloses structures and make the carbohydrates accessible for more efficient bioconversion. White-rot fungi produce ligninolytic enzymes (lignin peroxidase, manganese peroxidase, and laccase) and efficiently mineralise lignin into CO2 and H2O. Biological pretreatment of lignocelluloses using white-rot fungi has been used for decades for ruminant feed, enzymatic hydrolysis, and biopulping. Application of white-rot fungi capabilities can offer environmentally friendly processes for utilising lignocelluloses over physical or chemical pretreatment. This paper reviews white-rot fungi, ligninolytic enzymes, the effect of biological pretreatment on biomass characteristics, and factors affecting biological pretreatment. Application of biological pretreatment for enzymatic hydrolysis, biofuels (bioethanol, biogas and pyrolysis), biopulping, biobleaching, animal feed, and enzymes production are also discussed. Keywords: Biological pretreatment; White-rot fungi; Lignocellulose; Solid-state fermentation; Lignin peroxidase; -
Textile Dye Biodecolorization by Manganese Peroxidase: a Review
molecules Review Textile Dye Biodecolorization by Manganese Peroxidase: A Review Yunkang Chang 1,2, Dandan Yang 2, Rui Li 2, Tao Wang 2,* and Yimin Zhu 1,* 1 Institute of Environmental Remediation, Dalian Maritime University, Dalian 116026, China; [email protected] 2 The Lab of Biotechnology Development and Application, School of Biological Science, Jining Medical University, No. 669 Xueyuan Road, Donggang District, Rizhao 276800, China; [email protected] (D.Y.); [email protected] (R.L.) * Correspondence: [email protected] (T.W.); [email protected] (Y.Z.); Tel.: +86-063-3298-3788 (T.W.); +86-0411-8472-6992 (Y.Z.) Abstract: Wastewater emissions from textile factories cause serious environmental problems. Man- ganese peroxidase (MnP) is an oxidoreductase with ligninolytic activity and is a promising biocatalyst for the biodegradation of hazardous environmental contaminants, and especially for dye wastewater decolorization. This article first summarizes the origin, crystal structure, and catalytic cycle of MnP, and then reviews the recent literature on its application to dye wastewater decolorization. In addition, the application of new technologies such as enzyme immobilization and genetic engineering that could improve the stability, durability, adaptability, and operating costs of the enzyme are highlighted. Finally, we discuss and propose future strategies to improve the performance of MnP-assisted dye decolorization in industrial applications. Keywords: manganese peroxidase; biodecolorization; dye wastewater; immobilization; recombi- nant enzyme Citation: Chang, Y.; Yang, D.; Li, R.; Wang, T.; Zhu, Y. Textile Dye Biodecolorization by Manganese Peroxidase: A Review. Molecules 2021, 26, 4403. https://doi.org/ 1. Introduction 10.3390/molecules26154403 The textile industry produces large quantities of wastewater containing different types of dyes used during the dyeing process, which cause great harm to the environment [1,2]. -
New Automatically Built Profiles for a Better Understanding of the Peroxidase Superfamily Evolution
University of Geneva Practical training report submitted for the Master Degree in Proteomics and Bioinformatics New automatically built profiles for a better understanding of the peroxidase superfamily evolution presented by Dominique Koua Supervisors: Dr Christophe DUNAND Dr Nicolas HULO Laboratory of Plant Physiology, Dr Christian J.A. SIGRIST University of Geneva Swiss Institute of Bioinformatics PROSITE group. Geneva, April, 18th 2008 Abstract Motivation: Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. These proteins are extremely widespread and present in almost all living organisms. An important number of haem and non-haem peroxidase sequences are annotated and classified in the peroxidase database PeroxiBase (http://peroxibase.isb-sib.ch). PeroxiBase contains about 5800 peroxidase sequences classified as haem peroxidases and non-haem peroxidases and distributed between thirteen superfamilies and fifty subfamilies, (Passardi et al., 2007). However, only a few classification tools are available for the characterisation of peroxidase sequences: InterPro motifs, PRINTS and specifically designed PROSITE profiles. However, these PROSITE profiles are very global and do not allow the differenciation between very close subfamily sequences nor do they allow the prediction of specific cellular localisations. Due to the rapid growth in the number of available sequences, there is a need for continual updates and corrections of peroxidase protein sequences as well as for new tools that facilitate acquisition and classification of existing and new sequences. Currently, the PROSITE generalised profile building manner and their usage do not allow the differentiation of sequences from subfamilies showing a high degree of similarity. -
Characterization of Lignin-Modifying Enzymes of the Selective White-Rot
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Helsingin yliopiston digitaalinen arkisto Characterization of the lignin-modifying enzymes of the selective white-rot fungus Physisporinus rivulosus Terhi K. Hakala Department of Applied Chemistry and Microbiology Division of Microbiology Faculty of Agriculture and Forestry and Viikki Graduate School in Biosciences University of Helsinki Academic dissertation To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public criticism in Auditorium 1, Viikki Infocenter, Viikinkaari 11, on October 19th 2007 at 12 o’clock noon. Helsinki 2007 Supervisor: Professor Annele Hatakka Department of Applied Chemistry and Microbiology University of Helsinki Finland Reviewers: Docent Kristiina Kruus VTT Espoo, Finland Professor Martin Hofrichter Environmental Biotechnology International Graduate School Zittau, Germany Opponent: Professor Kurt Messner Institute of Chemical Engineering Vienna University of Technology Wien, Austria ISSN 1795-7079 ISBN 978-952-10-4172-3 (paperback) ISBN 978-952-10-4173-0 (PDF) Helsinki University Printing House Helsinki 2007 Cover photo: Spruce wood chips (KCL, Lea Kurlin) 2 Contents Contents..................................................................................................................................................3 List of original publications....................................................................................................................4 -
Ioides Species Kazuhiro Takagi, Kunihiko Fujii, Ken-Ichi Yamazaki, Naoki Harada and Akio Iwasaki Download PDF (313.9 KB) View HTML
Aquaculture Journals – Table of Contents With the financial support of Flemish Interuniversity Councel Aquaculture Journals – Table of Contents September 2012 Information of interest !! Animal Feed Science and Technology * Antimicrobial Agents and Chemotherapy Applied and Environmental Microbiology Applied Microbiology and Biotechnology Aqua Aquaculture * Aquaculture Economics & Management Aquacultural Engineering * Aquaculture International * Aquaculture Nutrition * Aquaculture Research * Current Opinion in Microbiology * Diseases of Aquatic Organisms * Fish & Shellfish Immunology * Fisheries Science * Hydrobiologia * Indian Journal of Fisheries International Journal of Aquatic Science Journal of Applied Ichthyology * Journal of Applied Microbiology * Journal of Applied Phycology Journal of Aquaculture Research and Development Journal of Experimental Marine Biology and Ecology * Journal of Fish Biology Journal of Fish Diseases * Journal of Invertebrate Pathology* Journal of Microbial Ecology* Aquaculture Journals Page: 1 of 331 Aquaculture Journals – Table of Contents Journal of Microbiological Methods Journal of Shellfish Research Journal of the World Aquaculture Society Letters in Applied Microbiology * Marine Biology * Marine Biotechnology * Nippon Suisan Gakkaishi Reviews in Aquaculture Trends in Biotechnology * Trends in Microbiology * * full text available Aquaculture Journals Page: 2 of 331 Aquaculture Journals – Table of Contents BibMail Information of Interest - September, 2012 Abstracts of papers presented at the XV International