Identification and Determination of Antioxidant Constituents Of
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Kotlobay Et Al. 10.1073/Pnas.1803615115
Supplementary materials for Kotlobay et al. 10.1073/pnas.1803615115 Supplementary Methods Molecular biology Identification of the nnluz gene. To achieve strong constitutive expression of cDNA library from Neonothopanus nambi, we constructed the GAP-pPic9K vector. The plasmid was created based on pPic9K vector (Invitrogen) by replacing inducible alcohol oxidase promoter AOX1 and alpha-factor signal sequences with the glyceraldehydes-3-phosphate dehydrogenase (GAP) promoter from Pichia pastoris. GAP promoter sequence was obtained from the vector pGAPZA by digestion with BglII, completion of overhanging nucleotides with Klenow fragment and subsequent digestion with EcoRI. pPic9K vector was digested with AatII, blunted with Klenow fragment, subsequently digested with EcoRI and used as a backbone for cloning of GAP promoter fragment. Unique restriction sites BamHI, Eco53kI, SacI were further introduced by PCR with primers 5’-AATTGGATCCCAGAGGCTCGC-3’ and 5’-GGCCGCGAGCTCTGGGATCC-3’ and cloning with EcoRI/NotI sites. Total RNA from N.nambi mycelium was prepared according to the protocol from Chomczynski and Sacchi (1987) [ref. (1)] and the cDNA library was constructed with SMART PCR cDNA Synthesis Kit (Clontech). Amplified cDNA was cloned into the GAP-pPic9K vector using BamHI/NotI restriction sites. pPic9K vector spontaneously generate multiple insertion events after linearization, as linear DNA can generate stable transformants of Pichia pastoris via homologous recombination between the transforming DNA and regions of homology within the genome (2–4). Multiple insertion events occur spontaneously 10-100 times less often than single insertion events (GAP-pPic9K vector manual, ThermoFisher). Extracted cDNA plasmid library was linearized by AvrII restriction site and used for transformation of Pichia pastoris GS115 strain by electroporation. -
Announcement Nampijja 4.5.21
Plant Pathology Seminar Series Bioluminescent fungi, a source of genes to monitor plant stresses and changes in the environment Marilen Nampijja, PhD student Bioluminescence is a natural phenomenon of light emission by a living organism resulting from oxidation of luciferin catalyzed by the enzyme luciferase (Dubois 1887). This process serves as a powerful biological tool for scientists to study gene expression in plants and animals. A wide diversity of living organisms is bioluminescent, including some fungi (Shimomura 2006). For many of these organisms, the ability to emit light is a defining feature of their biology (Labella et al. 2017; Verdes and Gruber 2017; Wainwright and https://www.sentinelassam.com Longo 2017). For example, bioluminescence in many organisms serves purposes such as attracting mates and pollinators, scaring predators, and recruiting other creatures to spread spores (Kotlobay et al. 2018; Shimomura 2006; Verdes and Gruber 2017). Oliveira and Stevani (2009) confirmed that the fungal bioluminescent reaction involved reduction of luciferin by NADPH and a luciferase. Their findings supported earlier studies by Airth and McElroy (1959) who found that the addition of reduced pyridine nucleotide and NADPH resulted in sustained light emission using the standard luciferin-luciferase test developed by Dubois (1887). Additionally, Kamzolkina et al. (1984;1983) and Kuwabara and Wassink (1966) purified and crystallized luciferin from the fungus Omphalia flavida, which was active in bioluminescence when exposed to the enzyme prepared according to the procedure described by Airth and McElroy (1959). Decades after, Kotlobay et al. (2018) showed that the fungal luciferase is encoded by the luz gene and three other key enzymes that form a complete biosynthetic cycle of the fungal luciferin from caffeic acid. -
Filamentous Fungi Diversity in the Natural Fermentation of Amazonian Cocoa Beans and the Microbial Enzyme Activities
Annals of Microbiology (2019) 69:975–987 https://doi.org/10.1007/s13213-019-01488-1 ORIGINAL ARTICLE Filamentous fungi diversity in the natural fermentation of Amazonian cocoa beans and the microbial enzyme activities Jean Aquino de Araújo1 & Nelson Rosa Ferreira1 & Silvia Helena Marques da Silva2 & Guilherme Oliveira 3 & Ruan Campos Monteiro4 & Yamila Fernandes Mota Alves1 & Alessandra Santos Lopes1 Received: 18 September 2018 /Revised: 13 May 2019 /Accepted: 29 May 2019 /Published online: 20 June 2019 # Università degli studi di Milano 2019 Abstract Purpose The purpose of this study was to investigate the diversity of filamentous fungi and the hydrolytic potential of their enzymes for a future understanding of the influence of these factors on the sensory characteristics of the cocoa beans used to obtain chocolate. Methods Filamentous fungi were isolated from the natural cocoa fermentation boxes in the municipality of Tucuman, Pará, Brazil, and evaluated for the potential production of amylases, cellulases, pectinases, and xylanases. The fermentation was monitored by analyzing the pH and temperature. The strains were identified by sequencing the ITS1/ITS4 section of the 5.8S rDNA and partially sequencing the 18S and 28S regions, and the molecular identification was confirmed by phylogenetic reconstruction. Result The fungi isolated were comprised of three classes from the Ascomycota phylum and one class from the Basidiomycota phylum. There were found 19 different species, of this amount 16 had never been previously reported in cocoa fermentation. This fact characterizes the fermentation occurring in this municipality as having wide fungal diversity. Most of the strains isolated had the ability to secrete enzymes of interest. -
New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences
Journal of Fungi Article New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences Lene Lange 1, Kristian Barrett 2 and Anne S. Meyer 2,* 1 BioEconomy, Research & Advisory, Copenhagen, 2500 Valby, Denmark; [email protected] 2 Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; [email protected] * Correspondence: [email protected]; Tel.: +45-4525-2600 Abstract: Fungal genome sequencing data represent an enormous pool of information for enzyme dis- covery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate- active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked accord- ing to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several pro- tein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme Citation: Lange, L.; Barrett, K.; hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host Meyer, A.S. -
73 Supplementary Data Genbank Accession Numbers Species Name
73 Supplementary Data The phylogenetic distribution of resupinate forms across the major clades of homobasidiomycetes. BINDER, M., HIBBETT*, D. S., LARSSON, K.-H., LARSSON, E., LANGER, E. & LANGER, G. *corresponding author: [email protected] Clades (C): A=athelioid clade, Au=Auriculariales s. str., B=bolete clade, C=cantharelloid clade, Co=corticioid clade, Da=Dacymycetales, E=euagarics clade, G=gomphoid-phalloid clade, GL=Gloephyllum clade, Hy=hymenochaetoid clade, J=Jaapia clade, P=polyporoid clade, R=russuloid clade, Rm=Resinicium meridionale, T=thelephoroid clade, Tr=trechisporoid clade, ?=residual taxa as (artificial?) sister group to the athelioid clade. Authorities were drawn from Index Fungorum (http://www.indexfungorum.org/) and strain numbers were adopted from GenBank (http://www.ncbi.nlm.nih.gov/). GenBank accession numbers are provided for nuclear (nuc) and mitochondrial (mt) large and small subunit (lsu, ssu) sequences. References are numerically coded; full citations (if published) are listed at the end of this table. C Species name Authority Strain GenBank accession References numbers nuc-ssu nuc-lsu mt-ssu mt-lsu P Abortiporus biennis (Bull.) Singer (1944) KEW210 AF334899 AF287842 AF334868 AF393087 4 1 4 35 R Acanthobasidium norvegicum (J. Erikss. & Ryvarden) Boidin, Lanq., Cand., Gilles & T623 AY039328 57 Hugueney (1986) R Acanthobasidium phragmitis Boidin, Lanq., Cand., Gilles & Hugueney (1986) CBS 233.86 AY039305 57 R Acanthofungus rimosus Sheng H. Wu, Boidin & C.Y. Chien (2000) Wu9601_1 AY039333 57 R Acanthophysium bisporum Boidin & Lanq. (1986) T614 AY039327 57 R Acanthophysium cerussatum (Bres.) Boidin (1986) FPL-11527 AF518568 AF518595 AF334869 66 66 4 R Acanthophysium lividocaeruleum (P. Karst.) Boidin (1986) FP100292 AY039319 57 R Acanthophysium sp. -
Genetically Encodable Bioluminescent System from Fungi
Genetically encodable bioluminescent system from fungi Alexey A. Kotlobaya,1, Karen S. Sarkisyana,b,c,d,1,2, Yuliana A. Mokrushinaa,1, Marina Marcet-Houbene,f,1, Ekaterina O. Serebrovskayaa,1, Nadezhda M. Markinaa,b,g, Louisa Gonzalez Somermeyerc, Andrey Y. Gorokhovatskya, Andrey Vvedenskya, Konstantin V. Purtovh, Valentin N. Petushkovh, Natalja S. Rodionovah, Tatiana V. Chepurnyha, Liliia I. Fakhranurovai, Elena B. Guglyaj, Rustam Ziganshina, Aleksandra S. Tsarkovaa,j, Zinaida M. Kaskovaa,j, Victoria Shendera, Maxim Abakumovj,k, Tatiana O. Abakumoval, Inna S. Povolotskayaj, Fedor M. Eroshkina, Andrey G. Zaraiskya, Alexander S. Mishina, Sergey V. Dolgova, Tatiana Y. Mitiouchkinaa,b, Eugene P. Kopantzeva, Hans E. Waldenmaierm, Anderson G. Oliveiran, Yuichi Obao, Ekaterina Barsovaa,g, Ekaterina A. Bogdanovaa, Toni Gabaldóne,f,p, Cassius V. Stevaniq, Sergey Lukyanova,j, Ivan V. Smirnova, Josef I. Gitelsonh, Fyodor A. Kondrashovc, and Ilia V. Yampolskya,b,j,2 aShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; bPlanta LLC, 121205 Moscow, Russia; cInstitute of Science and Technology Austria, 3400 Klosterneuburg, Austria; dMedical Research Council London Institute of Medical Sciences, Imperial College London, W12 0NN London, United Kingdom; eCentre for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; fUniversitat Pompeu Fabra, 08003 Barcelona, Spain; gEvrogen JSC, 117997 Moscow, Russia; hInstitute of Biophysics, Federal Research Center Krasnoyarsk -
Neocampanella, a New Corticioid Fungal Genus, and a Note on Dendrothe/E Bispora
875 Neocampanella, a new corticioid fungal genus, and a note on Dendrothe/e bispora Karen K. Nakasone, David S. Hibbett, and Greta Goranova Abstract: The new genus Neocampanella (Agaricales, Agaricomycetes, Basidiomycota) is established for Dentocorticium blastanos Boidin & Gilles, a crustose species, and the new combination, Neocampanella blastanos, is proposed. Morpho logical and molecular studies support the recognition of the new genus and its close ties to Campanella, a pleurotoid aga ric. The recently described Brunneocorticium is a monotypic, corticioid genus closely related to Campanella also. Brunneocorticium pyrifonne S.H. Wu is conspecific with Dendrothele bispora Burds. & Nakasone, and the new combina tion, Brunneocorticium bisporum, is proposed. Key words: Dendrothele, dendrohyphidia, Marasmiaceae, sterile white basidiomycete, Tetrapyrgos. Resume: Les auteurs proposent Ie nouveau genre Neocampanella (Agaricales, Agaromycetes, Basidiomycetes, Basidio mycota) etabli pour le Dentocorticium blastanos Boidin & Gilles, une espece resupinee ainsi que la nouvelle combinaison, Neocampanella blastanos. Les etudes morphologiques et moleculaires supportent la delimitation du nouveau genre, ainsi que ses etroites relations avec Campanella, un agaric pleurotoide, Le genre Brunneocorticium recemment decrit constitue une entire monotypique corticoide egalement apparentee au Neocampanella. Le Brunneocorticium pyriforme S.H. Wu est conspecifique au Dendrothele bispora Burds. & Nakasone pour lequel I' on propose la nouvelle combinaison B. bisporum. Mots-des: Dendrothele, dendrophidia, Marasmiaceae, basidiomycete blanc steriles, Tetrapyrgos. [Traduit par la Redaction] Introduction odiscus (Wu et al. 2001) were shown to be polyphyletic by molecular methods and analyses. Corticioid basidiomycetes have simple, reduced fruiting bodies that often appear as thin, crustose areas on bark and Introduced in 1907, Dendrothele Hohn. & Litsch. is a cor woody substrates. -
Unambiguous Identification of Fungi: Where Do We Stand and How Accurate and Precise Is Fungal DNA Barcoding? Robert Lücking1,2* , M
Lücking et al. IMA Fungus (2020) 11:14 https://doi.org/10.1186/s43008-020-00033-z IMA Fungus NOMENCLATURE Open Access Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? Robert Lücking1,2* , M. Catherine Aime2,3 , Barbara Robbertse4, Andrew N. Miller2,5 , Hiran A. Ariyawansa2,6 , Takayuki Aoki2,7 , Gianluigi Cardinali8 , Pedro W. Crous2,9,10 , Irina S. Druzhinina2,11,12 , David M. Geiser13, David L. Hawksworth2,14,15,16,17 ,KevinD.Hyde2,18,19,20,21 , Laszlo Irinyi22 , Rajesh Jeewon23 , Peter R. Johnston2,24 , Paul M. Kirk25 , Elaine Malosso2,26 ,TomW.May2,27 , Wieland Meyer22 ,MaarjaÖpik2,28 ,VincentRobert8,9, Marc Stadler2,29 ,MarcoThines2,30 , Duong Vu9 ,AndreyM.Yurkov2,31 ,NingZhang2,32 and Conrad L. Schoch2,4 ABSTRACT True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. -
Immunomodulatory Effects of Edible and Medicinal Mushrooms and Their Bioactive Immunoregulatory Products
Journal of Fungi Review Immunomodulatory Effects of Edible and Medicinal Mushrooms and Their Bioactive Immunoregulatory Products Shuang Zhao 1, Qi Gao 1, Chengbo Rong 1, Shouxian Wang 1, Zhekun Zhao 1,2, Yu Liu 1 and Jianping Xu 3,* 1 Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; [email protected] (S.Z.); [email protected] (Q.G.); [email protected] (C.R.); [email protected] (S.W.); [email protected] (Z.Z.); [email protected] (Y.L.) 2 College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China 3 Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada * Correspondence: [email protected] Received: 10 October 2020; Accepted: 2 November 2020; Published: 8 November 2020 Abstract: Mushrooms have been valued as food and health supplements by humans for centuries. They are rich in dietary fiber, essential amino acids, minerals, and many bioactive compounds, especially those related to human immune system functions. Mushrooms contain diverse immunoregulatory compounds such as terpenes and terpenoids, lectins, fungal immunomodulatory proteins (FIPs) and polysaccharides. The distributions of these compounds differ among mushroom species and their potent immune modulation activities vary depending on their core structures and fraction composition chemical modifications. Here we review the current status of clinical studies on immunomodulatory activities of mushrooms and mushroom products. The potential mechanisms for their activities both in vitro and in vivo were summarized. We describe the approaches that have been used in the development and application of bioactive compounds extracted from mushrooms. These developments have led to the commercialization of a large number of mushroom products. -
Bioluminescence: Chemical Study on Visible Light Emission from Fungal Mycelium and Fruiting Body
Trends in Technical & Scientific Research Mini-Review Trends Tech Sci Res Volume 1 Issue 3 - March 2018 Copyright © All rights are reserved by Katsunori Teranishi Bioluminescence: Chemical Study on Visible Light Emission from Fungal Mycelium and Fruiting Body Katsunori Teranishi* Graduate School of Bioresources, Mie University, Japan Submission: March 19, 2018; Published: March 28, 2018 *Corresponding author: Katsunori Teranishi, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie, Japan, Tel: ; Email: Abstract Although the visible light emission by living organisms is generally thought to be rare, in fact the bioluminescent phenomenon can be widely observed in nature, for examples insects, fishes, bacteria, and fungi. The phenomenon has intrigued scientific researchers over the years. agriculture,The chemical biology, mechanisms ecology, underlying and medicine. bioluminescence However, many differ other between bioluminescence species. Some mechanisms mechanisms, yet remain such as to bioluminescence be understood. Further of firefly, research jellyfish, of bacteria, and dinoflagellate, have been elucidated and further more their principles have allowed the development of many novel technologies in underlying fungal bioluminescence, which are actively in progress. bioluminescence will lead discoveries of biological significance and novel possibility in science. Here I present studies on chemical mechanism Keywords: Bioluminescence; Chemiluminescence; Fungus; Luciferin; Luciferase; Mechanism Mini Review Bioluminescence -
Gymnopus Acervatus</Em> (Agaricales)
University of Tennessee, Knoxville Trace: Tennessee Research and Creative Exchange Ecology and Evolutionary Biology Publications and Ecology and Evolutionary Biology Other Works 2010 A new genus to accommodate Gymnopus acervatus (Agaricales) Karen Hughes University of Tennessee - Knoxville David A. Mather Ronald H. Peterson Follow this and additional works at: http://trace.tennessee.edu/utk_ecolpubs Part of the Population Biology Commons Recommended Citation Hughes, Karen; Mather, David A.; and Peterson, Ronald H., "A new genus to accommodate Gymnopus acervatus (Agaricales)" (2010). Ecology and Evolutionary Biology Publications and Other Works. http://trace.tennessee.edu/utk_ecolpubs/9 This Article is brought to you for free and open access by the Ecology and Evolutionary Biology at Trace: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Ecology and Evolutionary Biology Publications and Other Works by an authorized administrator of Trace: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Mycologia, 102(6), 2010, pp. 1463–1478. DOI: 10.3852/09-318 # 2010 by The Mycological Society of America, Lawrence, KS 66044-8897 A new genus to accommodate Gymnopus acervatus (Agaricales) Karen W. Hughes1 eastern North America and western Europe. In David A. Mather traditional morphology-based systematic treatments Ronald H. Petersen of Agaricales (more recently known as euagarics) Ecology and Evolutionary Biology, University of Agaricus acervatus Fries has been among species Tennessee, Knoxville, Tennessee 37996-1100 considered ‘‘collybioid’’. Once Fries (1836:92) recog- nized segregate genera from Agaricus, A. acervatus was accepted as belonging in subg. Levipedes of Abstract: Phylogenies based on ITS and LSU nrDNA Collybia.Ku¨hner and Romagnesi (1953) included sequences show Agaricus (Gymnopus) acervatus as M. -
Estimating Levels of Light Emission and Extracellular Peroxidase Activity of Mycelium of Luminous Fungus Neonothopanus Nambi Treated with Β-Glucosidase
Current Research in Environmental & Applied Mycology (Journal of Fungal Biology) 8(1): 75–85 (2018) ISSN 2229-2225 www.creamjournal.org Article Doi 10.5943/cream/8/1/6 Copyright © Beijing Academy of Agriculture and Forestry Sciences Estimating levels of light emission and extracellular peroxidase activity of mycelium of luminous fungus Neonothopanus nambi treated with β-glucosidase Mogilnaya OA*, Ronzhin NO and Bondar VS Institute of Biophysics, Siberian Branch of Russian Academy of Science, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia Mogilnaya OA, Ronzhin NO, Bondar VS 2018 – Estimating levels of light emission and extracellular peroxidase activity of mycelium of luminous fungus Neonothopanus nambi treated with β-glucosidase. Current Research in Environmental & Applied Mycology (Journal of Fungal Biology) 8(1), 75–85, Doi 10.5943/cream/8/1/6 Abstract The present study estimates the level of extracellular peroxidase activity and light emission intensity of mycelium of luminescent basidiomycete Neonothopanus nambi treated with β- glucosidase. A hypothesis has been proposed that treatment with β-glucosidase may trigger biochemical mechanisms of activation of ROS (primarily hydrogen peroxide) generation in N. nambi mycelium. The results obtained indicate that the enzyme causes partial disintegration of the slimy sheath of fungal hyphae and intracellular matrix, which leads to release of the extracellular peroxidases to the incubation medium. Mycelial cells treated with the enzyme reach the peak of their luminescence sooner. It has been assumed that partial loss of extracellular peroxidases, as important enzymes of antioxidant defense, may be compensated for by an increase in the level of light emission by the fungus.