The Burkholderia Genus: Between Mutualism and Pathogenicity
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Evolution Toward Maximum Transport Capacity of the Ttg2 ABC System In
bioRxiv preprint doi: https://doi.org/10.1101/834812; this version posted November 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. 1 Evolution toward maximum transport capacity of the Ttg2 ABC system in 2 Pseudomonas aeruginosa 3 4 Daniel Yero,1,2 Lionel Costenaro,1# Oscar Conchillo-Solé,1 Mireia Díaz-Lobo,3 Adrià 5 Mayo,1 Mario Ferrer-Navarro,1# Marta Vilaseca,3 Isidre Gibert,1,2* Xavier Daura1,4* 6 7 1Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona 8 (UAB), Barcelona, Spain; 9 2Departament de Genètica i de Microbiologia, UAB, Barcelona, Spain; 10 3Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of 11 Science and Technology, Barcelona, Spain; 12 4Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain. 13 14 *Corresponding Authors: Xavier Daura, Tel: (+34)935868940 Email: 15 [email protected]. Isidre Gibert, Tel: (+34)935862050 Email: 16 [email protected]. 17 18 #Present address: Lionel Costenaro, Institut de Biologia Molecular de Barcelona 19 (CSIC), Barcelona, Spain. Mario Ferrer-Navarro, Teknokroma Analítica SA, 20 Barcelona, Spain. 21 1 bioRxiv preprint doi: https://doi.org/10.1101/834812; this version posted November 8, 2019. 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. 22 Abstract 23 In Pseudomonas aeruginosa, Ttg2D is the soluble periplasmic phospholipid-binding 24 component of an ABC transport system thought to be involved in maintaining the 25 asymmetry of the outer membrane. -
Multilayered Horizontal Operon Transfers from Bacteria Reconstruct a Thiamine Salvage Pathway in Yeasts
Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts Carla Gonçalvesa and Paula Gonçalvesa,1 aApplied Molecular Biosciences Unit-UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved September 22, 2019 (received for review June 14, 2019) Horizontal acquisition of bacterial genes is presently recognized as nisms presumed to have facilitated a transition from bacterial an important contribution to the adaptation and evolution of operon transcription to eukaryotic-style gene expression were eukaryotic genomes. However, the mechanisms underlying ex- proposed, such as gene fusion giving rise to multifunctional pro- pression and consequent selection and fixation of the prokaryotic teins (6, 23, 24), increase in intergenic distances between genes to genes in the new eukaryotic setting are largely unknown. Here we generate room for eukaryotic promoters, and independent tran- show that genes composing the pathway for the synthesis of the scription producing mRNAs with poly(A) tails have been dem- essential vitamin B1 (thiamine) were lost in an ancestor of a yeast onstrated (22). In the best documented study, which concerns a lineage, the Wickerhamiella/Starmerella (W/S) clade, known to bacterial siderophore biosynthesis operon acquired by yeasts be- harbor an unusually large number of genes of alien origin. The longing to the Wickerhamiella/Starmerella (W/S) clade, the bacte- thiamine pathway was subsequently reassembled, at least twice, rial genes acquired as an operon were shown to be functional (22). by multiple HGT events from different bacterial donors involving Thiamine, commonly known as vitamin B1, is essential for all both single genes and entire operons. -
Burkholderia Cenocepacia Integrates Cis-2-Dodecenoic Acid and Cyclic Dimeric Guanosine Monophosphate Signals to Control Virulence
Burkholderia cenocepacia integrates cis-2-dodecenoic acid and cyclic dimeric guanosine monophosphate signals to control virulence Chunxi Yanga,b,c,d,1, Chaoyu Cuia,b,c,1, Qiumian Yea,b, Jinhong Kane, Shuna Fua,b, Shihao Songa,b, Yutong Huanga,b, Fei Hec, Lian-Hui Zhanga,c, Yantao Jiaf, Yong-Gui Gaod, Caroline S. Harwoodb,g,2, and Yinyue Denga,b,c,2 aState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; bGuangdong Innovative Research Team of Sociomicrobiology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; cIntegrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; dSchool of Biological Sciences, Nanyang Technological University, Singapore 637551; eCenter for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; fState Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and gDepartment of Microbiology, University of Washington, Seattle, WA 98195 Contributed by Caroline S. Harwood, October 30, 2017 (sent for review June 1, 2017; reviewed by Maxwell J. Dow and Tim Tolker-Nielsen) Quorum sensing (QS) signals are used by bacteria to regulate N-octanoyl homoserine lactone (C8-HSL). The two QS systems biological functions in response to cell population densities. Cyclic have both distinct and overlapping effects on gene expression diguanosine monophosphate (c-di-GMP) regulates cell functions in (16, 17). response to diverse environmental chemical and physical signals One of the ways in which QS systems can act is by controlling that bacteria perceive. In Burkholderia cenocepacia, the QS signal levels of intracellular cyclic diguanosine monophosphate (c-di-GMP) receptor RpfR degrades intracellular c-di-GMP when it senses the in bacteria (18–21). -
Resilience of Microbial Communities After Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
microorganisms Article Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms Tim Piel 1,†, Giovanni Sandrini 1,†,‡, Gerard Muyzer 1 , Corina P. D. Brussaard 1,2 , Pieter C. Slot 1, Maria J. van Herk 1, Jef Huisman 1 and Petra M. Visser 1,* 1 Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; [email protected] (T.P.); [email protected] (G.S.); [email protected] (G.M.); [email protected] (C.P.D.B.); [email protected] (P.C.S.); [email protected] (M.J.v.H.); [email protected] (J.H.) 2 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands * Correspondence: [email protected]; Tel.: +31-20-5257073 † These authors have contributed equally to this work. ‡ Current address: Department of Technology & Sources, Evides Water Company, 3006 AL Rotterdam, The Netherlands. Abstract: Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little Citation: Piel, T.; Sandrini, G.; is known about the impacts of these H2O2 treatments on other members of the microbial com- Muyzer, G.; Brussaard, C.P.D.; Slot, munity. In this study, we investigated changes in microbial community composition during two P.C.; van Herk, M.J.; Huisman, J.; −1 lake treatments with low H2O2 concentrations (target: 2.5 mg L ) and in two series of controlled Visser, P.M. -
Burkholderia Cenocepacia Intracellular Activation of the Pyrin
Activation of the Pyrin Inflammasome by Intracellular Burkholderia cenocepacia Mikhail A. Gavrilin, Dalia H. A. Abdelaziz, Mahmoud Mostafa, Basant A. Abdulrahman, Jaykumar Grandhi, This information is current as Anwari Akhter, Arwa Abu Khweek, Daniel F. Aubert, of September 29, 2021. Miguel A. Valvano, Mark D. Wewers and Amal O. Amer J Immunol 2012; 188:3469-3477; Prepublished online 24 February 2012; doi: 10.4049/jimmunol.1102272 Downloaded from http://www.jimmunol.org/content/188/7/3469 Supplementary http://www.jimmunol.org/content/suppl/2012/02/24/jimmunol.110227 Material 2.DC1 http://www.jimmunol.org/ References This article cites 71 articles, 17 of which you can access for free at: http://www.jimmunol.org/content/188/7/3469.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 29, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2012 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Activation of the Pyrin Inflammasome by Intracellular Burkholderia cenocepacia Mikhail A. -
Genomic Plasticity of the Causative Agent of Melioidosis, Burkholderia Pseudomallei
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei Matthew T. G. Holdena, Richard W. Titballb,c, Sharon J. Peacockd,e, Ana M. Cerden˜ o-Ta´ rragaa, Timothy Atkinsb, Lisa C. Crossmana, Tyrone Pittf, Carol Churchera, Karen Mungalla, Stephen D. Bentleya, Mohammed Sebaihiaa, Nicholas R. Thomsona, Nathalie Basona, Ifor R. Beachamg, Karen Brooksa, Katherine A. Brownh, Nat F. Browng, Greg L. Challisi, Inna Cherevacha, Tracy Chillingwortha, Ann Cronina, Ben Crossetth, Paul Davisa, David DeShazerj, Theresa Feltwella, Audrey Frasera, Zahra Hancea, Heidi Hausera, Simon Holroyda, Kay Jagelsa, Karen E. Keithh, Mark Maddisona, Sharon Moulea, Claire Pricea, Michael A. Quaila, Ester Rabbinowitscha, Kim Rutherforda, Mandy Sandersa, Mark Simmondsa, Sirirurg Songsivilaik, Kim Stevensa, Sarinna Tumapae, Monkgol Vesaratchaveste, Sally Whiteheada, Corin Yeatsa, Bart G. Barrella, Petra C. F. Oystonb, and Julian Parkhilla,l aWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; bDefence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, United Kingdom; cDepartment of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom; dNuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, United Kingdom; eFaculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; fLaboratory of Hospital Infection, Division of Nosocomial Infection Prevention and Control, Central Public Health Laboratory, London NW9 5HT, United Kingdom; gSchool of Health Science, Griffith University, Gold Coast, Queensland 9726, Australia; hDepartment of Biological Sciences, Centre for Molecular Microbiology and Infection, Flowers Building, Imperial College, London SW7 2AZ, United Kingdom; iDepartment of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom; jU.S. -
Improved Bacterial Recombineering by Parallelized Protein Discovery
Improved bacterial recombineering by parallelized protein discovery Timothy M. Wanniera,1, Akos Nyergesa,b, Helene M. Kuchwaraa, Márton Czikkelyb, Dávid Baloghb, Gabriel T. Filsingera, Nathaniel C. Bordersa, Christopher J. Gregga, Marc J. Lajoiea, Xavier Riosa, Csaba Pálb, and George M. Churcha,1 aDepartment of Genetics, Harvard Medical School, Boston, MA 02115; and bSynthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary Edited by Susan Gottesman, National Institutes of Health, Bethesda, MD, and approved April 17, 2020 (received for review January 30, 2020) Exploiting bacteriophage-derived homologous recombination pro- recombineering, is the molecular mechanism that drives MAGE cesses has enabled precise, multiplex editing of microbial genomes and DIvERGE (4, 32, 33). This method was first described in and the construction of billions of customized genetic variants in a E. coli, and is most commonly promoted by the expression of bet single day. The techniques that enable this, multiplex automated ge- (here referred to as Redβ) from the Red operon of Escherichia nome engineering (MAGE) and directed evolution with random ge- phage λ (5, 6, 34). Redβ is an ssDNA-annealing protein (SSAP) nomic mutations (DIvERGE), are however, currently limited to a whose role in recombineering is to anneal ssDNA to compli- handful of microorganisms for which single-stranded DNA-annealing mentary genomic DNA at the replication fork. Although im- proteins (SSAPs) that promote efficient recombineering have been provements to recombineering efficiency have been made (7–9), identified. Thus, to enable genome-scale engineering in new hosts, the core protein machinery has remained constant, with Redβ efficient SSAPs must first be found. -
Lung Microbiota Changes Associated with Chronic Pseudomonas Aeruginosa Lung Infection and the Impact Of
Edinburgh Research Explorer Lung Microbiota Changes Associated with Chronic Pseudomonas aeruginosa Lung Infection and the Impact of Intravenous Colistimethate Sodium Citation for published version: Collie, D, Glendinning, L, Govan, J, Wright, S, Thornton, E, Tennant, P, Doherty, C & McLachlan, G 2015, 'Lung Microbiota Changes Associated with Chronic Pseudomonas aeruginosa Lung Infection and the Impact of Intravenous Colistimethate Sodium' PLoS One, vol. 10, no. 11, pp. e0142097. DOI: 10.1371/journal.pone.0142097 Digital Object Identifier (DOI): 10.1371/journal.pone.0142097 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: PLoS One Publisher Rights Statement: © 2015 Collie et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact -
Characterization of the Burkholderia Cenocepacia J2315 Surface-Exposed Immunoproteome
Article Characterization of the Burkholderia cenocepacia J2315 Surface-Exposed Immunoproteome 1, 1, 1, Sílvia A. Sousa * , António M.M. Seixas y , Manoj Mandal y, Manuel J. Rodríguez-Ortega 2 and Jorge H. Leitão 1,* 1 iBB–Institute for Bioengineering and Biosciences, 1049-001 Lisbon, Portugal; [email protected] (A.M.M.S.); [email protected] (M.M.) 2 Departament of Biochemistry and Molecular Biology, Córdoba University, 14071 Córdoba, Spain; [email protected] * Correspondence: [email protected] (S.A.S.); [email protected] (J.H.L.); Tel.: +351-2184-19986 (S.A.S.); +351-2184-17688 (J.H.L.) Both authors contributed equally to the work. y Received: 31 July 2020; Accepted: 3 September 2020; Published: 6 September 2020 Abstract: Infections by the Burkholderia cepacia complex (Bcc) remain seriously life threatening to cystic fibrosis (CF) patients, and no effective eradication is available. A vaccine to protect patients against Bcc infections is a highly attractive therapeutic option, but none is available. A strategy combining the bioinformatics identification of putative surface-exposed proteins with an experimental approach encompassing the “shaving” of surface-exposed proteins with trypsin followed by peptide identification by liquid chromatography and mass spectrometry is here reported. The methodology allowed the bioinformatics identification of 263 potentially surface-exposed proteins, 16 of them also experimentally identified by the “shaving” approach. Of the proteins identified, 143 have a high probability of containing B-cell epitopes that are surface-exposed. The immunogenicity of three of these proteins was demonstrated using serum samples from Bcc-infected CF patients and Western blotting, validating the usefulness of this methodology in identifying potentially immunogenic surface-exposed proteins that might be used for the development of Bcc-protective vaccines. -
The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia Sp
fmicb-11-00581 April 19, 2020 Time: 8:50 # 1 ORIGINAL RESEARCH published: 21 April 2020 doi: 10.3389/fmicb.2020.00581 The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato Johannes B. Herpell1, Florian Schindler1, Mersad Bejtovic´ 1, Lena Fragner1,2, Bocar Diallo1, Anke Bellaire3, Susanne Kublik4, Bärbel U. Foesel4, Silvia Gschwendtner4, Melina Kerou5, Michael Schloter4 and Wolfram Weckwerth1,2* 1 Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria, 2 Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria, 3 Division of Structural and Functional Botany, Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria, 4 Research Unit Edited by: for Comparative Microbiome Analysis, German Research Center for Environmental Health, Helmholtz Zentrum München, 5 Michele Perazzolli, Neuherberg, Germany, Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Trento, Italy University of Vienna, Vienna, Austria Reviewed by: Stéphane Compant, The genus Paraburkholderia includes a variety of species with promising features for Austrian Institute of Technology (AIT), sustainable biotechnological solutions in agriculture through increasing crop productivity. Austria Lionel Moulin, Here, we present a novel Paraburkholderia isolate, a permanent and predominant Institut de Recherche Pour le member of the Dioscoreae bulbifera (yam family, Dioscoreaceae) -
Targeting the Burkholderia Cepacia Complex
viruses Review Advances in Phage Therapy: Targeting the Burkholderia cepacia Complex Philip Lauman and Jonathan J. Dennis * Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-780-492-2529 Abstract: The increasing prevalence and worldwide distribution of multidrug-resistant bacterial pathogens is an imminent danger to public health and threatens virtually all aspects of modern medicine. Particularly concerning, yet insufficiently addressed, are the members of the Burkholderia cepacia complex (Bcc), a group of at least twenty opportunistic, hospital-transmitted, and notoriously drug-resistant species, which infect and cause morbidity in patients who are immunocompromised and those afflicted with chronic illnesses, including cystic fibrosis (CF) and chronic granulomatous disease (CGD). One potential solution to the antimicrobial resistance crisis is phage therapy—the use of phages for the treatment of bacterial infections. Although phage therapy has a long and somewhat checkered history, an impressive volume of modern research has been amassed in the past decades to show that when applied through specific, scientifically supported treatment strategies, phage therapy is highly efficacious and is a promising avenue against drug-resistant and difficult-to-treat pathogens, such as the Bcc. In this review, we discuss the clinical significance of the Bcc, the advantages of phage therapy, and the theoretical and clinical advancements made in phage therapy in general over the past decades, and apply these concepts specifically to the nascent, but growing and rapidly developing, field of Bcc phage therapy. Keywords: Burkholderia cepacia complex (Bcc); bacteria; pathogenesis; antibiotic resistance; bacterio- phages; phages; phage therapy; phage therapy treatment strategies; Bcc phage therapy Citation: Lauman, P.; Dennis, J.J.