DOCSLIB.ORG

Bacterial Comparative Genomics

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Bacterial Comparative Genomics CENTRO DE INVESTIGACION Y DE ESTUDIOS AVANZADOS DEL INSTITUTO POLITECNICO NACIONAL UNIDAD IRAPUATO “Explorando los mecanismos moleculares que mantienen la simbiosis Rhizopus microsporus – Burkholderia rhizoxinica” Presenta LCG José Roberto Bermúdez Barrientos Para obtener el grado de Maestro en Ciencias en Biología Integrativa Directores de tesis: Dra. Laila Pamela Partida Martínez Dr. Cei Leander Gastón Abreu Goodger Irapuato, Guanajuato Febrero de 2016 1 CENTRO DE INVESTIGACION Y DE ESTUDIOS AVANZADOS DEL INSTITUTO POLITECNICO NACIONAL UNIDAD IRAPUATO “Exploring the molecular mechanisms maintaining the Rhizopus microsporus - Burkholderia rhizoxinica symbiosis” Presents LCG José Roberto Bermúdez Barrientos To obtain the grade of Master in Sciences in Integrative Biology Thesis directors: Dr. Laila Pamela Partida Martínez Dr. Cei Leander Gastón Abreu Goodger Irapuato, Guanajuato February de 2016 2 Agracecimientos Este trabajo se realizó en el Centro de Investigación y de Estudios Avanzados del IPN - Unidad Irapuato. Bajo la dirección de Dra. Laila Pamela Partida Martínez y de Dr. Cei Abreu Goodger En el Laboratorio de Interacciones Microbianas perteneciente al Departamento de Ingeniería Genética y en el Laboratorio de Genómica computacional del RNA perteneciente a la Unidad de Genómica Avanzada. En colaboración con la Dra Teresa Pawlowska, Plant Pathology & Plant-Microbe Biology Lab, Plant Science Department, Cornell University, Ithaca, NY. Gracias al apoyo del Consejo Nacional de Ciencia y Tecnología (CONACyT) a través de los Proyectos CB-2009-01-133388, CB-2010-01-151007, INFR-2012-01- 187799 y la beca 358014 Este trabajo se realizó del 1 de Septiembre de 2013 al 1 de Octubre de 2015 Miembros del comité de asesores: Dr. Alfredo Herrera Estrella, Unidad de Genómica Avanzada, CINVESTAV Irapuato Dr. Luis Delaye Arredondo, Departamento de Ingeniería Genética, CINVESTAV Irapuato 3 Acknowledgements This project was realized at Centro de Investigación y de Estudios Avanzados del IPN – Unidad Irapuato Under the direction of Dr. Laila Pamera Partida Martínez and Dr. Cei Abreu Goodger At the Laboratory of Microbial Interactions belonging to Departamento de Ingeniería Genética and at the RNA Computational Genomics Laboratory belonging to the Unidad de Genómica Avanzada In colaboration with Dr. Teresa Pawlowska, Plant Pathology & Plant-Microbe Biology Lab, Plant Science Department, Cornell University, Ithaca, NY. Thanks to the support given by Consejo Nacional de Ciencia y Tecnología (CONACyT) through projects CB-2009-01-133388, CB-2010-01-151007, INFR- 2012-01-187799 and the scholarship 358014 This project was realized from September 1st of 2013 to October 1st of 2016 Committee members: Dr. Alfredo Herrera Estrella, Unidad de Genómica Avanzada, CINVESTAV Irapuato Dr. Luis Delaye Arredondo, Departamento de Ingeniería Genética, CINVESTAV Irapuato Thanks: To my advisors, Dr. Laila Partida and Dr. Cei Abreu: for their guidance and being crucial players in my formation To my committee members: Dr. Alfredo Herrera Estrella and Dr. Luis Delaye Arredondo for their valuable comments, discussions and suggestions To Stephen Jay Mondo and Teresa E. Pawlowska for sharing their RNA-Seq data with us, and being such great hosts to me in Ithaca To my family for their unconditional love and support To my all friends for the moments we shared in this adventure To my lab partners for their support 4 Contents LIST OF ABREVIATIONS .................................................................................................... 7 ABSTRACT .......................................................................................................................... 8 RESUMEN ............................................................................................................................ 9 CHAPTER I: INTRODUCTION & BACKGROUND ........................................................... 11 ENDOSYMBIOSIS: CONCEPTS & HISTORICAL BACKGROUND ................................................. 11 MYCOVIRUSES ................................................................................................................. 14 The Narnaviridae family of Mycovirus ......................................................................... 16 EUKARYOTIC CHROMATIN MANIPULATION BY BACTERIA ...................................................... 17 Chromatin ................................................................................................................... 17 Chromatin structure and regulation ............................................................................ 18 Histone modification language .................................................................................... 19 Histone variants .......................................................................................................... 21 Host chromatin manipulation by pathogens and symbionts ....................................... 21 FUNGAL IMMUNITY AND SYMBIONT PERCEPTION ................................................................. 23 Leucine rich repeats ................................................................................................... 23 Lysin motif ................................................................................................................... 24 TOXIN-ANTITOXIN SYSTEMS ............................................................................................... 24 NON-RIBOSOMAL PEPTIDE SYNTHETASES ......................................................................... 26 THE RHIZOPUS MICROSPORUS – BURKHOLDERIA RHIZOXINICA SYMBIOSIS .......................... 29 OBJECTIVE ....................................................................................................................... 33 SPECIFIC OBJECTIVES ....................................................................................................... 33 JUSTIFICATION ................................................................................................................ 34 DIFFERENTIAL EXPRESSION ANALYSIS ............................................................................... 34 COMPARATIVE GENOMICS ................................................................................................. 34 CHAPTER II: METHODS ................................................................................................... 35 ANNOTATIONS .................................................................................................................. 36 Pfam ........................................................................................................................... 36 GO .............................................................................................................................. 36 RAST .......................................................................................................................... 37 AntiSMASH ................................................................................................................. 37 RNA-SEQ ANALYSIS ......................................................................................................... 38 Experimental design, extraction & sequencing ........................................................... 38 Quality control ............................................................................................................. 40 Mapping ...................................................................................................................... 40 Gene counts ............................................................................................................... 41 Differential Expression Analysis ................................................................................. 41 B. rhizoxinica expression inside its host ..................................................................... 42 Tracing the origin of a high-GC peak .......................................................................... 42 FUNGAL COMPARATIVE GENOMICS .................................................................................... 44 Defining protein families in Mucorales ........................................................................ 46 Mucorales phylogeny reconstruction .......................................................................... 46 Comparison of protein domains in fungi ..................................................................... 47 BACTERIAL COMPARATIVE GENOMICS ................................................................................ 49 Defining protein families in Burkholderia .................................................................... 51 Burkholderia core genome & phylogeny ..................................................................... 51 Functional categories comparison .............................................................................. 52 Search for Burkholderia toxin-antitoxin proteins in Mucorales .................................... 54 5 CHAPTER III: RNA-SEQ ANALYSIS RESULTS .............................................................. 55 NARNAVIRUSES IN RHIZOPUS ............................................................................................ 55 A strange peak of reads with high-GC content ........................................................... 55 Tracing peak origin and discovery of Narnavirus sequences ..................................... 59 GENERAL LIBRARIES DESCRIPTION .................................................................................... 60 HOUSEKEEPING
Load more

Recommended publications
  • Iron Transport Strategies of the Genus Burkholderia
    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2015 Iron transport strategies of the genus Burkholderia Mathew, Anugraha Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-113412 Dissertation Published Version Originally published at: Mathew, Anugraha. Iron transport strategies of the genus Burkholderia. 2015, University of Zurich, Faculty of Science. Iron transport strategies of the genus Burkholderia Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultät der Universität Zürich von Anugraha Mathew aus Indien Promotionskomitee Prof. Dr. Leo Eberl (Vorsitz) Prof. Dr. Jakob Pernthaler Dr. Aurelien carlier Zürich, 2015 2 Table of Contents Summary .............................................................................................................. 7 Zusammenfassung ................................................................................................ 9 Abbreviations ..................................................................................................... 11 Chapter 1: Introduction ....................................................................................... 14 1.1.Role and properties of iron in bacteria ...................................................................... 14 1.2.Iron transport mechanisms in bacteria .....................................................................
    [Show full text]
  • Broad-Spectrum Antimicrobial Activity by Burkholderia Cenocepacia Tatl-371, a Strain Isolated from the Tomato Rhizosphere
    RESEARCH ARTICLE Rojas-Rojas et al., Microbiology DOI 10.1099/mic.0.000675 Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere Fernando Uriel Rojas-Rojas,1 Anuar Salazar-Gómez,1 María Elena Vargas-Díaz,1 María Soledad Vasquez-Murrieta, 1 Ann M. Hirsch,2,3 Rene De Mot,4 Maarten G. K. Ghequire,4 J. Antonio Ibarra1,* and Paulina Estrada-de los Santos1,* Abstract The Burkholderia cepacia complex (Bcc) comprises a group of 24 species, many of which are opportunistic pathogens of immunocompromised patients and also are widely distributed in agricultural soils. Several Bcc strains synthesize strain- specific antagonistic compounds. In this study, the broad killing activity of B. cenocepacia TAtl-371, a Bcc strain isolated from the tomato rhizosphere, was characterized. This strain exhibits a remarkable antagonism against bacteria, yeast and fungi including other Bcc strains, multidrug-resistant human pathogens and plant pathogens. Genome analysis of strain TAtl-371 revealed several genes involved in the production of antagonistic compounds: siderophores, bacteriocins and hydrolytic enzymes. In pursuit of these activities, we observed growth inhibition of Candida glabrata and Paraburkholderia phenazinium that was dependent on the iron concentration in the medium, suggesting the involvement of siderophores. This strain also produces a previously described lectin-like bacteriocin (LlpA88) and here this was shown to inhibit only Bcc strains but no other bacteria. Moreover, a compound with an m/z 391.2845 with antagonistic activity against Tatumella terrea SHS 2008T was isolated from the TAtl-371 culture supernatant. This strain also contains a phage-tail-like bacteriocin (tailocin) and two chitinases, but the activity of these compounds was not detected.
    [Show full text]
  • Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome
    bioRxiv preprint doi: https://doi.org/10.1101/780619; this version posted September 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Horizontal gene transfer to a defensive symbiont with a reduced genome 2 amongst a multipartite beetle microbiome 3 Samantha C. Waterwortha, Laura V. Flórezb, Evan R. Reesa, Christian Hertweckc,d, 4 Martin Kaltenpothb and Jason C. Kwana# 5 6 Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin- 7 Madison, Madison, Wisconsin, USAa 8 Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, 9 Johannes Gutenburg University, Mainz, Germanyb 10 Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research 11 and Infection Biology, Jena, Germanyc 12 Department of Natural Product Chemistry, Friedrich Schiller University, Jena, Germanyd 13 14 #Address correspondence to Jason C. Kwan, [email protected] 15 16 17 18 1 bioRxiv preprint doi: https://doi.org/10.1101/780619; this version posted September 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 19 ABSTRACT 20 The loss of functions required for independent life when living within a host gives rise to 21 reduced genomes in obligate bacterial symbionts. Although this phenomenon can be 22 explained by existing evolutionary models, its initiation is not well understood.
    [Show full text]
  • Molecular Study of the Burkholderia Cenocepacia Division Cell Wall Operon and Ftsz Interactome As Targets for New Drugs
    Università degli Studi di Pavia Dipartimento di Biologia e Biotecnologie “L. Spallanzani” Molecular study of the Burkholderia cenocepacia division cell wall operon and FtsZ interactome as targets for new drugs Gabriele Trespidi Dottorato di Ricerca in Genetica, Biologia Molecolare e Cellulare XXXIII Ciclo – A.A. 2017-2020 Università degli Studi di Pavia Dipartimento di Biologia e Biotecnologie “L. Spallanzani” Molecular study of the Burkholderia cenocepacia division cell wall operon and FtsZ interactome as targets for new drugs Gabriele Trespidi Supervised by Prof. Edda De Rossi Dottorato di Ricerca in Genetica, Biologia Molecolare e Cellulare XXXIII Ciclo – A.A. 2017-2020 Cover image: representation of the Escherichia coli division machinery. Created by Ornella Trespidi A tutta la mia famiglia e in particolare a Diletta Table of contents Abstract ..................................................................................................... 1 Abbreviations ............................................................................................ 3 1. Introduction ........................................................................................... 5 1.1 Cystic fibrosis 5 1.1.1 CFTR defects in CF 5 1.1.2 Pathophysiology of CF 7 1.1.3 CFTR modulator therapies 11 1.2 CF-associated lung infections 12 1.2.1 Pseudomonas aeruginosa 13 1.2.2 Staphylococcus aureus 14 1.2.3 Stenotrophomonas maltophilia 15 1.2.4 Achromobacter xylosoxidans 16 1.2.5 Non-tuberculous mycobacteria 17 1.3 The genus Burkholderia 18 1.3.1 Burkholderia cepacia complex 20 1.3.2 Bcc species as CF pathogens 22 1.4 Burkholderia cenocepacia 23 1.4.1 B. cenocepacia epidemiology 23 1.4.2 B. cenocepacia genome 25 1.4.3 B. cenocepacia pathogenicity and virulence factors 26 1.4.3.1 Quorum sensing 29 1.4.3.2 Biofilm 32 1.4.4 B.
    [Show full text]
  • The Organization of the Quorum Sensing Luxi/R Family Genes in Burkholderia
    Int. J. Mol. Sci. 2013, 14, 13727-13747; doi:10.3390/ijms140713727 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article The Organization of the Quorum Sensing luxI/R Family Genes in Burkholderia Kumari Sonal Choudhary 1, Sanjarbek Hudaiberdiev 1, Zsolt Gelencsér 2, Bruna Gonçalves Coutinho 1,3, Vittorio Venturi 1,* and Sándor Pongor 1,2,* 1 International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 32149, Italy; E-Mails: [email protected] (K.S.C.); [email protected] (S.H.); [email protected] (B.G.C.) 2 Faculty of Information Technology, PázmányPéter Catholic University, Práter u. 50/a, Budapest 1083, Hungary; E-Mail: [email protected] 3 The Capes Foundation, Ministry of Education of Brazil, Cx postal 250, Brasilia, DF 70.040-020, Brazil * Authors to whom correspondence should be addressed; E-Mails: [email protected] (V.V.); [email protected] (S.P.); Tel.: +39-40-375-7300 (S.P.); Fax: +39-40-226-555 (S.P.). Received: 30 May 2013; in revised form: 20 June 2013 / Accepted: 24 June 2013 / Published: 2 July 2013 Abstract: Members of the Burkholderia genus of Proteobacteria are capable of living freely in the environment and can also colonize human, animal and plant hosts. Certain members are considered to be clinically important from both medical and veterinary perspectives and furthermore may be important modulators of the rhizosphere. Quorum sensing via N-acyl homoserine lactone signals (AHL QS) is present in almost all Burkholderia species and is thought to play important roles in lifestyle changes such as colonization and niche invasion.
    [Show full text]
  • Identification of the Essential Genome of Burkholderia Cenocepacia K56-2 to Uncover Novel
    Identification of the Essential Genome of Burkholderia cenocepacia K56-2 to Uncover Novel Antibacterial Targets by April S. Gislason A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Microbiology University of Manitoba Winnipeg, Manitoba, Canada Copyright © 2017 April S. Gislason ii Abstract Burkholderia cenocepacia K56-2 is a clinical isolate of the Burkholderia cepacia complex, a group of intrinsically antibiotic resistant opportunistic pathogens, for which few treatment options are available. The identification of essential genes is an important step for exploring new antibiotic targets. Previously, a conditional growth mutant library was created using transposon mutagenesis to insert a rhamnose-inducible promoter into the genome of B. cenocepacia. It was then demonstrated that conditional growth mutants under-expressing an antibiotic target were sensitized to sub-lethal concentrations of that antibiotic. This thesis describes the use of next generation sequencing to measure the enhanced sensitivity of conditional growth mutants after being grown together competitively. Evidence is provided to show that the sensitivity of a GyrB conditional growth mutant to its cognate antibiotic, novobiocin, was enhanced due to competitive growth. Screening eight antibiotics with known mechanisms of action against a pilot conditional growth mutant library revealed a previously uncharacterized two-component system involved antibiotic resistance in B. cenocepacia. With the goal of exploring new Burkholderia antibacterial targets, the essential genome of B. cenocepacia K56-2 was identified by sequencing a high density transposon mutant library. Comparison of the B. cenocepacia K56-2 essential gene set with the essential genomes predicted for B.
    [Show full text]
  • Diazotrophic Burkholderia Species Isolated from the Amazon Region Exhibit
    Systematic and Applied Microbiology 35 (2012) 253–262 Contents lists available at SciVerse ScienceDirect Systematic and Applied Microbiology jo urnal homepage: www.elsevier.de/syapm Diazotrophic Burkholderia species isolated from the Amazon region exhibit phenotypical, functional and genetic diversity a,1,2 b,3 b,3 c,4 Krisle da Silva , Alice de Souza Cassetari , Adriana Silva Lima , Evie De Brandt , d c,4 b,∗ Eleanor Pinnock , Peter Vandamme , Fatima Maria de Souza Moreira a Microbiologia Agrícola Graduate Programme, Departamento de Biologia, Universidade Federal de Lavras, Campus UFLA, 37200-000 Lavras, Minas Gerais, Brazil b Laboratório de Biologia, Microbiologia e Processos Biológicos do Solo, Departamento de Ciência do Solo, Universidade Federal de Lavras, Campus UFLA, 37200-000 Lavras, Minas Gerais, Brazil c Laboratorium voor Microbiologie, Faculteit Wetenschappen, Universiteit Gent, K. L. Ledeganckstraat 35, 9000 Gent, Belgium d Department of Biological Sciences, Warwick University, Coventry CV4 7AL, United Kingdom a r t i c l e i n f o a b s t r a c t Article history: Forty-eight Burkholderia isolates from different land use systems in the Amazon region were compared Received 25 January 2012 to type strains of Burkholderia species for phenotypic and functional characteristics that can be used Received in revised form 21 April 2012 to promote plant growth. Most of these isolates (n = 46) were obtained by using siratro (Macroptilium Accepted 24 April 2012 atropurpureum – 44) and common bean (Phaseolus vulgaris –2) as the trap plant species; two isolates were obtained from nodules collected in the field from Indigofera suffruticosa and Pithecellobium sp. The Keywords: evaluated characteristics were the following: colony characterisation on “79” medium, assimilation of Macroptilium atropurpureum different carbon sources, enzymatic activities, solubilisation of phosphates, nitrogenase activity and anti- Phaseolus vulgaris fungal activity against Fusarium oxysporium f.
    [Show full text]
  • The Evolutionary Diversity and Biological Function of Phenazine Metabolite Biosynthesis in Burkholderia SPP
    The University of Southern Mississippi The Aquila Digital Community Master's Theses Summer 2019 The Evolutionary Diversity and Biological Function of Phenazine Metabolite Biosynthesis in Burkholderia SPP Samuel Hendry University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/masters_theses Part of the Bacteriology Commons Recommended Citation Hendry, Samuel, "The Evolutionary Diversity and Biological Function of Phenazine Metabolite Biosynthesis in Burkholderia SPP" (2019). Master's Theses. 653. https://aquila.usm.edu/masters_theses/653 This Masters Thesis is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Master's Theses by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. THE EVOLUTIONARY DIVERSITY AND BIOLOGICAL FUNCTION OF PHENAZINE METABOLITE BIOSYNTHESIS IN BURKHOLDERIA SPP by Samuel Hendry A Thesis Submitted to the Graduate School, the College of Arts and Sciences and the School of Biological, Environmental, and Earth Sciences at The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Master of Science Approved by: Dmitri Mavrodi, Committee Chair Janet Donaldson Mohamed Elasri ____________________ ____________________ ____________________ Dr. Dmitri Mavrodi Dr. Jake Schaefer Dr. Karen S. Coats Committee Chair Director of School Dean of the Graduate School August 2019 COPYRIGHT BY Samuel Hendry 2019 Published by the Graduate School ABSTRACT Burkholderia encompass a group of ubiquitous Gram-negative bacteria that include numerous saprophytes, as well as several species that cause infections in animals, immunocompromised patients, and plants. Some species of Burkholderia produce colored redox-active secondary metabolites called phenazines (Phz).
    [Show full text]
  • Genomic Analysis of the Potential for Aromatic Compounds
    bs_bs_banner Environmental Microbiology (2012) 14(5), 1091–1117 doi:10.1111/j.1462-2920.2011.02613.x Minireview Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderialesemi_2613 1091..1117 Danilo Pérez-Pantoja,1 Raúl Donoso,1,2 in the catabolic clusters of these pathways indicating Loreine Agulló,3 Macarena Córdova,3 recent events in its evolutionary history. In addition, a Michael Seeger,3 Dietmar H. Pieper4 and significant bias towards secondary chromosomes, Bernardo González1,2* now termed chromids, is observed in the distribution 1Center for Advanced Studies in Ecology and of catabolic genes across multipartite genomes, Biodiversity. Millennium Nucleus in Plant Functional which is consistent with a genus-specific character. Genomics. Facultad de Ciencias Biológicas, P. Strains isolated from environmental sources such as Universidad Católica de Chile. Santiago, Chile. soil, rhizosphere, sediment or sludge show a higher 2Facultad de Ingeniería y Ciencias, Universidad Adolfo content of catabolic genes in their genomes com- Ibáñez. Santiago, Chile. pared with strains isolated from human, animal or 3Laboratorio de Microbiología Molecular y Biotecnología plant hosts, but no significant difference is found Ambiental, Departamento de Química, Center for among Alcaligenaceae, Burkholderiaceae and Coma- Nanotechnology and Systems Biology, Universidad monadaceae families, indicating that habitat is more Técnica Federico Santa María, Valparaíso, Chile. of a determinant than phylogenetic origin in shaping 4Microbial Interactions and Processes Research Group, aromatic catabolic versatility. Department of Medical Microbiology, HZI – Helmholtz Centre for Infection Research. Braunschweig, Germany. Introduction Aromatic compounds are widespread in nature, being Summary found as lignin and petroleum components, xenobiotic The relevance of the b-proteobacterial Burkholderi- chemicals, aromatic amino acids and constituents of plant ales order in the degradation of a vast array of exudates, among other sources.
    [Show full text]
  • Research Article Burkholderia Contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes
    Hindawi Publishing Corporation BioMed Research International Volume 2016, Article ID 6560534, 13 pages http://dx.doi.org/10.1155/2016/6560534 Research Article Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes Olga L. Voronina,1 Marina S. Kunda,1 Natalia N. Ryzhova,1 Ekaterina I. Aksenova,1 Andrey N. Semenov,1 Yulia M. Romanova,1,2 and Alexandr L. Gintsburg1,2 1 N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Gamaleya Street 18, Moscow 123098, Russia 2I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia Correspondence should be addressed to Olga L. Voronina; [email protected] Received 24 February 2016; Accepted 8 November 2016 Academic Editor: Vassily Lyubetsky Copyright © 2016 Olga L. Voronina et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Biofilm formation by Burkholderia spp. is a principal cause of lung chronic infections in cystic fibrosis patients. A “lacking biofilm production” (LBP) strain B. contaminans GIMC4587:Bct370-19 has been obtained by insertion modification of clinical strain with plasposon mutagenesis. It has an interrupted transcriptional response regulator (RR) gene. The focus of our investigation was a two-component signal transduction system determination, including this RR. B. contaminans clinical and LBP strains were analyzed by whole genome sequencing and bioinformatics resources. A four-component operon (BiofilmReg) has a key role in biofilm formation. The relative location (i.e., by being separated by another gene) of RR and histidine kinase genes is uniquein BiofilmReg.
    [Show full text]
  • Burkholderia Bacteria Produce Multiple Potentially Novel Molecules That Inhibit Carbapenem-Resistant Gram-Negative Bacterial Pathogens
    antibiotics Article Burkholderia Bacteria Produce Multiple Potentially Novel Molecules that Inhibit Carbapenem-Resistant Gram-Negative Bacterial Pathogens Eliza Depoorter 1 , Evelien De Canck 1, Tom Coenye 2 and Peter Vandamme 1,* 1 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium; [email protected] (E.D.); [email protected] (E.D.C.) 2 Laboratory of Pharmaceutical Microbiology, Department of Pharmaceutical Analysis, Ghent University, 9000 Ghent, Belgium; [email protected] * Correspondence: [email protected]; Tel.: +32-9264-5113 Abstract: Antimicrobial resistance in Gram-negative pathogens represents a global threat to human health. This study determines the antimicrobial potential of a taxonomically and geographically diverse collection of 263 Burkholderia (sensu lato) isolates and applies natural product dereplication strategies to identify potentially novel molecules. Antimicrobial activity is almost exclusively present in Burkholderia sensu stricto bacteria and rarely observed in the novel genera Paraburkholderia, Caballero- nia, Robbsia, Trinickia, and Mycetohabitans. Fourteen isolates show a unique spectrum of antimicrobial activity and inhibited carbapenem-resistant Gram-negative bacterial pathogens. Dereplication of the molecules present in crude spent agar extracts identifies 42 specialized metabolites, 19 of which repre- sented potentially novel molecules. The known identified Burkholderia metabolites include toxoflavin, reumycin, pyrrolnitrin,
    [Show full text]
  • Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis
    Curr Microbiol DOI 10.1007/s00284-013-0330-9 Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis Paulina Estrada-de los Santos • Pablo Vinuesa • Lourdes Martı´nez-Aguilar • Ann M. Hirsch • Jesu´s Caballero-Mellado Received: 11 August 2012 / Accepted: 21 January 2013 Ó Springer Science+Business Media New York 2013 Abstract Burkholderia comprises more than 60 species bacterial species. The group B comprises the B. cepacia of environmental, clinical, and agro-biotechnological rel- complex (opportunistic human pathogens), the B. pseudo- evance. Previous phylogenetic analyses of 16S rRNA, mallei subgroup, which includes both human and animal recA, gyrB, rpoB, and acdS gene sequences as well as pathogens, and an assemblage of plant pathogenic species. genome sequence comparisons of different Burkholderia The distinct lineages present in Burkholderia suggest that species have revealed two major species clusters. In this each group might represent a different genus. However, it study, we undertook a multilocus sequence analysis of 77 will be necessary to analyze the full set of Burkholderia type and reference strains of Burkholderia using atpD, species and explore whether enough phenotypic features gltB, lepA, and recA genes in combination with the 16S exist among the different clusters to propose that these rRNA gene sequence and employed maximum likelihood groups should be considered separate genera. and neighbor-joining criteria to test this further. The phy- logenetic analysis revealed, with high supporting values, Abbreviations distinct lineages within the genus Burkholderia. The two MLSA Multilocus sequence analysis large groups were named A and B, whereas the B. rhi- BCC Burkholderia cepacia complex zoxinica/B.
    [Show full text]