223 Cyanogenic Glycosides and the Fate of Cyanide in Soil
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Recruitment of Genes and Enzymes Conferring Resistance to the Nonnatural Toxin Bromoacetate
Recruitment of genes and enzymes conferring resistance to the nonnatural toxin bromoacetate Kevin K. Desai and Brian G. Miller1 Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390 Edited* by Richard Wolfenden, University of North Carolina, Chapel Hill, NC, and approved August 24, 2010 (received for review May 28, 2010) Microbial niches contain toxic chemicals capable of forcing organ- tance of a naïve bacterial population can play a role in combating isms into periods of intense natural selection to afford survival. the toxicity of a nonnatural small-molecule. Revealing the reser- Elucidating the mechanisms by which microbes evade environmen- voir of intrinsic resistance genes that are subject to evolutionary tal threats has direct relevance for understanding and combating recruitment promises to aid our understanding of the processes the rise of antibiotic resistance. In this study we used a toxic small- leading to the emergence of antibiotic resistant pathogens. molecule, bromoacetate, to model the selective pressures imposed We sought to identify the full spectrum of bromoacetate resis- by antibiotics and anthropogenic toxins. We report the results tance mechanisms available to the model bacterium, Escherichia of genetic selection experiments that identify nine genes from coli. The reactivity of bromoacetate is likely to mimic that of elec- Escherichia coli whose overexpression affords survival in the trophilic natural products as well as anthropogenic environmen- presence of a normally lethal concentration of bromoacetate. Eight tal contaminants that microbes may encounter. The clinically of these genes encode putative transporters or transmembrane significant natural antibiotic fosfomycin, and the fungal natural proteins, while one encodes the essential peptidoglycan biosyn- product terreic acid, are electrophilic molecules that both target N thetic enzyme, UDP- -acetylglucosamine enolpyruvoyl transferase an essential nucleophilic cysteine residue in bacteria (8, 9). -
The Cyanide Hydratase from Neurospora Crassa Forms a Helix Which Has a Dimeric Repeat
Appl Microbiol Biotechnol (2009) 82:271–278 DOI 10.1007/s00253-008-1735-4 BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS The cyanide hydratase from Neurospora crassa forms a helix which has a dimeric repeat Kyle C. Dent & Brandon W. Weber & Michael J. Benedik & B. Trevor Sewell Received: 2 July 2008 /Revised: 24 September 2008 /Accepted: 25 September 2008 / Published online: 23 October 2008 # Springer-Verlag 2008 Abstract The fungal cyanide hydratases form a functionally Introduction specialized subset of the nitrilases which catalyze the hydrolysis of cyanide to formamide with high specificity. The generation of cyanide containing waste results from These hold great promise for the bioremediation of cyanide cyanide utilization in a variety of applications, spanning wastes. The low resolution (3.0 nm) three-dimensional such diverse industries as gold and silver mining, metal reconstruction of negatively stained recombinant cyanide electroplating, polymer synthesis, and the production of hydratase fibers from the saprophytic fungus Neurospora fine chemicals, pharmaceuticals, dyes, and agricultural crassa by iterative helical real space reconstruction reveals products (Baxter and Cummings 2006). Traditionally, that enzyme fibers display left-handed D1 S5.4 symmetry chemical oxidation or stabilizations are used to treat these with a helical rise of 1.36 nm. This arrangement differs from wastes; however, many groups have been studying the previously characterized microbial nitrilases which demon- potential for bioremediation of such cyanide waste strate a structure built along similar principles but with a (O’Reilly and Turner 2003; Jandhyala et al. 2005). reduced helical twist. The cyanide hydratase assembly is The most promising approach utilizes cyanide degrada- stabilized by two dyadic interactions between dimers across tion by enzymes belonging to the nitrilase family (Pace and the one-start helical groove. -
Cyanide-Degrading Enzymes for Bioremediation A
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Texas A&M University CYANIDE-DEGRADING ENZYMES FOR BIOREMEDIATION A Thesis by LACY JAMEL BASILE Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2008 Major Subject: Microbiology CYANIDE-DEGRADING ENZYMES FOR BIOREMEDIATION A Thesis by LACY JAMEL BASILE Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved by: Chair of Committee, Michael Benedik Committee Members, Susan Golden James Hu Wayne Versaw Head of Department, Vincent Cassone August 2008 Major Subject: Microbiology iii ABSTRACT Cyanide-Degrading Enzymes for Bioremediation. (August 2008) Lacy Jamel Basile, B.S., Texas A&M University Chair of Advisory Committee: Dr. Michael Benedik Cyanide-containing waste is an increasingly prevalent problem in today’s society. There are many applications that utilize cyanide, such as gold mining and electroplating, and these processes produce cyanide waste with varying conditions. Remediation of this waste is necessary to prevent contamination of soils and water. While there are a variety of processes being used, bioremediation is potentially a more cost effective alternative. A variety of fungal species are known to degrade cyanide through the action of cyanide hydratases, a specialized subset of nitrilases which hydrolyze cyanide to formamide. Here I report on previously unknown and uncharacterized nitrilases from Neurospora crassa, Gibberella zeae, and Aspergillus nidulans. Recombinant forms of four cyanide hydratases from N. -
Structures, Functions, and Mechanisms of Filament Forming Enzymes: a Renaissance of Enzyme Filamentation
Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation A Review By Chad K. Park & Nancy C. Horton Department of Molecular and Cellular Biology University of Arizona Tucson, AZ 85721 N. C. Horton ([email protected], ORCID: 0000-0003-2710-8284) C. K. Park ([email protected], ORCID: 0000-0003-1089-9091) Keywords: Enzyme, Regulation, DNA binding, Nuclease, Run-On Oligomerization, self-association 1 Abstract Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI system are also highlighted. 2 Contents INTRODUCTION…………………………………………………………..4 STRUCTURALLY CHARACTERIZED ENZYME FILAMENTS…….5 Acetyl CoA Carboxylase (ACC)……………………………………………………………………5 Phosphofructokinase (PFK)……………………………………………………………………….6 -
Changes in the Sclerotinia Sclerotiorum Transcriptome During Infection of Brassica Napus
Seifbarghi et al. BMC Genomics (2017) 18:266 DOI 10.1186/s12864-017-3642-5 RESEARCHARTICLE Open Access Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus Shirin Seifbarghi1,2, M. Hossein Borhan1, Yangdou Wei2, Cathy Coutu1, Stephen J. Robinson1 and Dwayne D. Hegedus1,3* Abstract Background: Sclerotinia sclerotiorum causes stem rot in Brassica napus, which leads to lodging and severe yield losses. Although recent studies have explored significant progress in the characterization of individual S. sclerotiorum pathogenicity factors, a gap exists in profiling gene expression throughout the course of S. sclerotiorum infection on a host plant. In this study, RNA-Seq analysis was performed with focus on the events occurring through the early (1 h) to the middle (48 h) stages of infection. Results: Transcript analysis revealed the temporal pattern and amplitude of the deployment of genes associated with aspects of pathogenicity or virulence during the course of S. sclerotiorum infection on Brassica napus. These genes were categorized into eight functional groups: hydrolytic enzymes, secondary metabolites, detoxification, signaling, development, secreted effectors, oxalic acid and reactive oxygen species production. The induction patterns of nearly all of these genes agreed with their predicted functions. Principal component analysis delineated gene expression patterns that signified transitions between pathogenic phases, namely host penetration, ramification and necrotic stages, and provided evidence for the occurrence of a brief biotrophic phase soon after host penetration. Conclusions: The current observations support the notion that S. sclerotiorum deploys an array of factors and complex strategies to facilitate host colonization and mitigate host defenses. This investigation provides a broad overview of the sequential expression of virulence/pathogenicity-associated genes during infection of B. -
Structural Characterization of Beta Carbonic Anhydrases from Higher Plants
Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 1998 Structural Characterization of Beta Carbonic Anhydrases From Higher Plants. Michael H. Bracey Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Bracey, Michael H., "Structural Characterization of Beta Carbonic Anhydrases From Higher Plants." (1998). LSU Historical Dissertations and Theses. 6655. https://digitalcommons.lsu.edu/gradschool_disstheses/6655 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type o f computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. -
Investigation of Iron's Role in Alginate Production And
INVESTIGATION OF IRON’S ROLE IN ALGINATE PRODUCTION AND MUCOIDY BY PSEUDOMONAS AERUGINOSA by JACINTA ROSE SCHRAUFNAGEL B.S., University of Colorado Denver, 2003 M.S., University of Colorado Denver, 2006 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirements for the degree of Doctor of Philosophy Molecular Biology Program 2013 This thesis for the Doctor of Philosophy degree by Jacinta Rose Schraufnagel has been approved for the Molecular Biology Program by David Barton, Chair Michael Vasil, Advisor Mair Churchill Jerry Schaack Michael Schurr Martin Voskuil Date 10/30/13 ii Schraufnagel, Jacinta R. (Ph.D., Molecular Biology) Investigation of Iron’s Role in Alginate Production and Mucoidy by Pseudomonas aeruginosa. Thesis directed by Professor Michael Vasil. ABSTRACT Iron, an essential nutrient, influences the production of major virulence factors and the development of structured non-alginate biofilms in Pseudomonas aeruginosa. Fur, pyoverdine and various concentrations of iron sources have all been shown to affect non-alginate biofilm formation. Remarkably however, the role of iron in alginate biofilm formation and mucoidy is unknown. Because of alginate’s association with biofilms in chronic cystic fibrosis (CF) lung infections, we examined the influence of iron on alginate production and mucoidy in P. aeruginosa. Herein, we identify and characterize a novel iron-regulated protein that affects the transcription of alginate biosynthesis genes. Further, contrary to what is known about non-alginate biofilms, we discovered that biologically relevant concentrations of iron (10 µM – 300 µM), in various forms (e.g. FeCl3, Ferric Citrate, Heme), led to the decreased expression of alginate biosynthesis genes and the dispersion of alginate biofilms in mucoid P. -
Tetranychus Urticae
UvA-DARE (Digital Academic Repository) The role of horizontally transferred genes in the xenobiotic adaptations of the spider mite Tetranychus urticae Wybouw, N.R. Publication date 2015 Document Version Final published version Link to publication Citation for published version (APA): Wybouw, N. R. (2015). The role of horizontally transferred genes in the xenobiotic adaptations of the spider mite Tetranychus urticae. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:03 Oct 2021 Nicky-ch2_Vera-ch1.qxd 18/08/2015 14:33 Page 41 2 A Horizontally Transferred Cyanase Gene in the Spider Mite Tetranychus urticae is Involved in Cyanate Metabolism and is Differentially Expressed Upon Host Plant Change N. Wybouw*, V. Balabanidou*, D.J. Ballhorn, W. -
Diversity of Antisense and Other Non-Coding Rnas in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species
Lawrence Berkeley National Laboratory Recent Work Title Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species. Permalink https://escholarship.org/uc/item/94r6n6t1 Journal Frontiers in microbiology, 3(JUL) ISSN 1664-302X Authors Bernick, David L Dennis, Patrick P Lui, Lauren M et al. Publication Date 2012 DOI 10.3389/fmicb.2012.00231 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH ARTICLE published: 02 July 2012 doi: 10.3389/fmicb.2012.00231 Diversity of antisense and other non-coding RNAs in archaea revealed by comparative small RNA sequencing in four Pyrobaculum species David L. Bernick 1, Patrick P.Dennis 2, Lauren M. Lui 1 andTodd M. Lowe 1* 1 Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA 2 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA Edited by: A great diversity of small, non-coding RNA (ncRNA) molecules with roles in gene regula- Frank T. Robb, University of California, tion and RNA processing have been intensely studied in eukaryotic and bacterial model USA organisms, yet our knowledge of possible parallel roles for small RNAs (sRNA) in archaea Reviewed by: Mircea Podar, Oak Ridge National is limited. We employed RNA-seq to identify novel sRNA across multiple species of the Laboratory, USA hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By Imke Schroeder, University of comparing transcriptional data collected in parallel among four species, we were able to California Los Angeles, USA identify conserved RNA genes fitting into known and novel families. -
Rnaseq Analysis of Aspergillus Fumigatus in Blood Reveals a Just Wait and See Resting Stage Behavior
Irmer et al. BMC Genomics (2015) 16:640 DOI 10.1186/s12864-015-1853-1 RESEARCH ARTICLE Open Access RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior Henriette Irmer1, Sonia Tarazona2, Christoph Sasse1, Patrick Olbermann4, Jürgen Loeffler5, Sven Krappmann4,6, Ana Conesa2,3 and Gerhard H. Braus1* Abstract Background: Invasive aspergillosis is started after germination of Aspergillus fumigatus conidia that are inhaled by susceptible individuals. Fungal hyphae can grow in the lung through the epithelial tissue and disseminate hematogenously to invade into other organs. Low fungaemia indicates that fungal elements do not reside in the bloodstream for long. Results: We analyzed whether blood represents a hostile environment to which the physiology of A. fumigatus has to adapt. An in vitro model of A. fumigatus infection was established by incubating mycelium in blood. Our model allowed to discern the changes of the gene expression profile of A. fumigatus at various stages of the infection. The majority of described virulence factors that are connected to pulmonary infections appeared not to be activated during the blood phase. Three active processes were identified that presumably help the fungus to survive the blood environment in an advanced phase of the infection: iron homeostasis, secondary metabolism, and the formation of detoxifying enzymes. Conclusions: We propose that A. fumigatus is hardly able to propagate in blood. After an early stage of sensing the environment, virtually all uptake mechanisms and energy-consuming metabolic pathways are shut-down. The fungus appears to adapt by trans-differentiation into a resting mycelial stage. -
Source: the Arabidopsis Information Resource (TAIR);
Table S1 List of targeted loci and information about their function in Arabidopsis thaliana (source: The Arabidopsis Information Resource (TAIR); https://www.arabidopsis.org/tools/bulk/genes/index.jsp). Locus Gene Model Gene Model Description Gene Model Primary Gene Symbol All Gene Symbols Identifier Name Type AT1G78800 AT1G78800.1 UDP-Glycosyltransferase superfamily protein_coding protein;(source:Araport11) AT5G06830 AT5G06830.1 hypothetical protein;(source:Araport11) protein_coding AT2G31740 AT2G31740.1 S-adenosyl-L-methionine-dependent methyltransferases protein_coding superfamily protein;(source:Araport11) AT5G11960 AT5G11960.1 magnesium transporter, putative protein_coding (DUF803);(source:Araport11) AT4G00560 AT4G00560.4 NAD(P)-binding Rossmann-fold superfamily protein_coding protein;(source:Araport11) AT1G80510 AT1G80510.1 Encodes a close relative of the amino acid transporter ANT1 protein_coding (AT3G11900). AT2G21250 AT2G21250.1 NAD(P)-linked oxidoreductase superfamily protein_coding protein;(source:Araport11) AT5G04420 AT5G04420.1 Galactose oxidase/kelch repeat superfamily protein_coding protein;(source:Araport11) AT4G34910 AT4G34910.1 P-loop containing nucleoside triphosphate hydrolases protein_coding superfamily protein;(source:Araport11) AT5G66120 AT5G66120.2 3-dehydroquinate synthase;(source:Araport11) protein_coding AT1G45110 AT1G45110.1 Tetrapyrrole (Corrin/Porphyrin) protein_coding Methylase;(source:Araport11) AT1G67420 AT1G67420.2 Zn-dependent exopeptidases superfamily protein_coding protein;(source:Araport11) AT3G62370 -
Viewed and Published Immediately Upon Acceptance Cited in Pubmed and Archived on Pubmed Central Yours — You Keep the Copyright
BMC Bioinformatics BioMed Central Methodology article Open Access Optimization based automated curation of metabolic reconstructions Vinay Satish Kumar1, Madhukar S Dasika2 and Costas D Maranas*2 Address: 1Department of Industrial and Manufacturing Engineering, The Pennsylvania State University, University Park, PA 16802, USA and 2Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA Email: Vinay Satish Kumar - [email protected]; Madhukar S Dasika - [email protected]; Costas D Maranas* - [email protected] * Corresponding author Published: 20 June 2007 Received: 14 December 2006 Accepted: 20 June 2007 BMC Bioinformatics 2007, 8:212 doi:10.1186/1471-2105-8-212 This article is available from: http://www.biomedcentral.com/1471-2105/8/212 © 2007 Satish Kumar et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis) with many more under development. All of these reconstructions are inherently incomplete with some functionalities missing due to the lack of experimental and/or homology information. A key challenge in the automated generation of genome-scale reconstructions is the elucidation of these gaps and the subsequent generation of hypotheses to bridge them. Results: In this work, an optimization based procedure is proposed to identify and eliminate network gaps in these reconstructions. First we identify the metabolites in the metabolic network reconstruction which cannot be produced under any uptake conditions and subsequently we identify the reactions from a customized multi-organism database that restores the connectivity of these metabolites to the parent network using four mechanisms.