Biologically Active Peptides from Marine Proteobacteria: Discussion Article
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Genomic Signatures of Predatory Bacteria
The ISME Journal (2013) 7, 756–769 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE By their genes ye shall know them: genomic signatures of predatory bacteria Zohar Pasternak1, Shmuel Pietrokovski2, Or Rotem1, Uri Gophna3, Mor N Lurie-Weinberger3 and Edouard Jurkevitch1 1Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel; 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel and 3Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the ‘predatome,’ that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. -
Pathogenic Mechanisms of Photobacterium Damselae Subspecies Piscicida in Hybrid Striped Bass Ahmad A
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2002 Pathogenic mechanisms of Photobacterium damselae subspecies piscicida in hybrid striped bass Ahmad A. Elkamel Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Veterinary Pathology and Pathobiology Commons Recommended Citation Elkamel, Ahmad A., "Pathogenic mechanisms of Photobacterium damselae subspecies piscicida in hybrid striped bass" (2002). LSU Doctoral Dissertations. 773. https://digitalcommons.lsu.edu/gradschool_dissertations/773 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 Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. PATHOGENIC MECHANISMS OF PHOTOBACTERIUM DAMSELAE SUBSPECIES PISCICIDA IN HYBRID STRIPED BASS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Pathobiological Sciences by Ahmad A. Elkamel B.V. Sc., Assiut University, 1993 May 2002 DEDICATION This work is dedicated to the people in my life who encouraged each step of my academic career. My mother was anxious as I was for each exam or presentation. I have been always looking to my Dad as a model, and trying to follow his footsteps in academic career. My wife stood by me like no other one in the world, and her love and support helped me see one of my dreams come true. -
Bismis-2016 Abstract Book
BISMiS-2016 Abstract Book Third Meeting of Bergey's International Society for Microbial Systematics on Microbial Systematics and Metagenomics September 12-15, 2016 | Pune, INDIA PUNE UNIT Abstracts - Opening Address - Keynotes Abstract Book | BISMiS-2016 | Pune, India Opening Address TAXONOMY OF PROKARYOTES - NEW CHALLENGES IN A GLOBAL WORLD Peter Kämpfer* Justus-Liebig-University Giessen, HESSEN, Germany Email: [email protected] Systematics can be considered as a comprehensive science, because in science it is an essential aspect in comparing any two or more elements, whether they are genes or genomes, proteins or proteomes, biochemical pathways or metabolomes (just to list a few examples), or whole organisms. The development of high throughput sequencing techniques has led to an enormous amount of data (genomic and other “omic” data) and has also revealed an extensive diversity behind these data. These data are more and more used also in systematics and there is a strong trend to classify and name the taxonomic units in prokaryotic systematics preferably on the basis of sequence data. Unfortunately, the knowledge of the meaning behind the sequence data does not keep up with the tremendous increase of generated sequences. The extent of the accessory genome in any given cell, and perhaps the infinite extent of the pan-genome (as an aggregate of all the accessory genomes) is fascinating but it is an open question if and how these data should be used in systematics. Traditionally the polyphasic approach in bacterial systematics considers methods including both phenotype and genotype. And it is the phenotype that is (also) playing an essential role in driving the evolution. -
A Genomic Journey Through a Genus of Large DNA Viruses
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Virology Papers Virology, Nebraska Center for 2013 Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses Adrien Jeanniard Aix-Marseille Université David D. Dunigan University of Nebraska-Lincoln, [email protected] James Gurnon University of Nebraska-Lincoln, [email protected] Irina V. Agarkova University of Nebraska-Lincoln, [email protected] Ming Kang University of Nebraska-Lincoln, [email protected] See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/virologypub Part of the Biological Phenomena, Cell Phenomena, and Immunity Commons, Cell and Developmental Biology Commons, Genetics and Genomics Commons, Infectious Disease Commons, Medical Immunology Commons, Medical Pathology Commons, and the Virology Commons Jeanniard, Adrien; Dunigan, David D.; Gurnon, James; Agarkova, Irina V.; Kang, Ming; Vitek, Jason; Duncan, Garry; McClung, O William; Larsen, Megan; Claverie, Jean-Michel; Van Etten, James L.; and Blanc, Guillaume, "Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses" (2013). Virology Papers. 245. https://digitalcommons.unl.edu/virologypub/245 This Article is brought to you for free and open access by the Virology, Nebraska Center for at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Virology Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Adrien Jeanniard, David D. Dunigan, James Gurnon, Irina V. Agarkova, Ming Kang, Jason Vitek, Garry Duncan, O William McClung, Megan Larsen, Jean-Michel Claverie, James L. Van Etten, and Guillaume Blanc This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ virologypub/245 Jeanniard, Dunigan, Gurnon, Agarkova, Kang, Vitek, Duncan, McClung, Larsen, Claverie, Van Etten & Blanc in BMC Genomics (2013) 14. -
Genus-Wide Comparison of Pseudovibrio Bacterial Genomes Reveal Diverse Adaptations to Different Marine Invertebrate Hosts
RESEARCH ARTICLE Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts Anoop Alex1,2*, Agostinho Antunes1,2* 1 CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal, 2 Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal * [email protected] (AA); [email protected] (AA) a1111111111 a1111111111 a1111111111 a1111111111 Abstract a1111111111 Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with OPEN ACCESS sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with Citation: Alex A, Antunes A (2018) Genus-wide other marine hosts has received less attention. Here, we performed genus-wide compara- comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine tive analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and sea- invertebrate hosts. PLoS ONE 13(5): e0194368. water. The analyses revealed a certain degree of commonality among the majority of https://doi.org/10.1371/journal.pone.0194368 sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tuni- Editor: Zhi Ruan, Zhejiang University, CHINA cates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities Received: November 12, 2017 including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flat- Accepted: March 1, 2018 worm-associated bacteria and the sponge-associated bacterium P. -
Isolation of an Antimicrobial Compound Produced by Bacteria Associated with Reef-Building Corals
A peer-reviewed version of this preprint was published in PeerJ on 18 August 2016. View the peer-reviewed version (peerj.com/articles/2275), which is the preferred citable publication unless you specifically need to cite this preprint. Raina J, Tapiolas D, Motti CA, Foret S, Seemann T, Tebben J, Willis BL, Bourne DG. 2016. Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals. PeerJ 4:e2275 https://doi.org/10.7717/peerj.2275 Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals Jean-Baptiste Raina Corresp., 1, 2, 3, 4, 5 , Dianne Tapiolas 2 , Cherie A Motti 2 , Sylvain Foret 3, 6 , Torsten Seemann 7 , Jan Tebben 8, 9 , Bette L Willis 3, 4 , David G Bourne 2, 4 1 Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia 2 Australian Institute of Marine Science, Townsville, QLD, Australia 3 James Cook University, Australian Research Council Centre of Excellence for Coral Reef Studies, Townsville, QLD, Australia 4 Marine Biology and Aquaculture, College of Science and Engineering, James Cook University of North Queensland, Townsville, QLD, Australia 5 James Cook University, AIMS@JCU, Townsville, QLD, Australia 6 Research School of Biology, Australian National University, Canberra, ACT, Australia 7 Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Victoria, Australia 8 Section Chemical Ecology, Alfred Wegener Institute, Bremerhaven, Germany 9 University of New South Wales, Sydney, NSW, Australia Corresponding Author: Jean-Baptiste Raina Email address: [email protected] Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. -
The Spot 42 RNA: a Regulatory Small RNA with Roles in the Central
1 The Spot 42 RNA: A regulatory small RNA with roles in the central 2 metabolism 3 Cecilie Bækkedal and Peik Haugen* 4 5 Department of Chemistry, The Norwegian Structural Biology Centre (NorStruct) and Centre for 6 Bioinformatics (SfB), UiT – The Arctic University of Norway, 9037 Tromsø, Norway 7 8 Key words: sRNA, small RNA, Spot 42, spf, non-coding RNA, gamma proteobacteria, pirin. 9 *Correspondence to: Peik Haugen; E-mail: [email protected] 10 Disclosure statement: the authors have no conflict of interest and nothing to disclose. 11 12 The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA 13 (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the 14 majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently 15 Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate 16 metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP 17 complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution 18 of spf, show family-specific secondary structural features of Spot 42, and link highly conserved 19 structural regions to mRNA target binding. 20 Introduction 21 The spf gene is highly conserved in Escherichia, Shigella, Klebsiella, Salmonella and Yersinia 22 (genera) within the Enterobacteriacea family.1 In E. coli the spf gene is flanked by polA 23 (upstream) and yihA (downstream),2,3 and a CRP binding sequence and -10 and -35 promoter 24 sequences are found upstream of spf. -
Lindane Bioremediation Capability of Bacteria Associated with the Demosponge Hymeniacidon Perlevis
marine drugs Article Lindane Bioremediation Capability of Bacteria Associated with the Demosponge Hymeniacidon perlevis Stabili Loredana 1,2,*, Pizzolante Graziano 2, Morgante Antonio 2, Nonnis Marzano Carlotta 3,4, Longo Caterina 3,4, Aresta Antonella Maria 5, Zambonin Carlo 5, Corriero Giuseppe 3,4 and Alifano Pietro 2 1 Istituto per l’Ambiente Marino Costiero, Unità Operativa di Supporto di Taranto, CNR, Via Roma 3, 74123 Taranto, Italy 2 Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy; [email protected] (P.G.); [email protected] (M.A.); [email protected] (A.P.) 3 Dipartimento di Biologia, Università di Bari Aldo Moro, 70125 Bari, Italy; [email protected] (N.M.C.); [email protected] (L.C.); [email protected] (C.G.) 4 CoNISMa, Piazzale Flaminio 9, 00196 Roma, Italy 5 Dipartimento di Chimica, Università di Bari Aldo Moro, 70125 Bari, Italy; [email protected] (A.A.M.); [email protected] (Z.C.) * Correspondence: [email protected]; Tel.: +39-0832-298971 Academic Editors: Vassilios Roussis, Efstathia Ioannou and Keith B. Glaser Received: 23 January 2017; Accepted: 27 March 2017; Published: 6 April 2017 Abstract: Lindane is an organochlorine pesticide belonging to persistent organic pollutants (POPs) that has been widely used to treat agricultural pests. It is of particular concern because of its toxicity, persistence and tendency to bioaccumulate in terrestrial and aquatic ecosystems. In this context, we assessed the role of bacteria associated with the sponge Hymeniacidon perlevis in lindane degradation. -
Physiology of Pseudovibrio Sp. FO-BEG1 – a Facultatively Oligotrophic and Metabolically Versatile Bacterium
Physiology of Pseudovibrio sp. FO-BEG1 – a facultatively oligotrophic and metabolically versatile bacterium Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Vladimir Bondarev Bremen, Februar 2012 Die vorliegende Arbeit wurde in der Zeit von Januar 2008 bis Februar 2012 am Max-Planck- Institut für Marine Mikrobiologie in Bremen angefertigt. 1. Gutachterin: Prof. Dr. Heide Schulz-Vogt 2. Gutachter: Prof. Dr. Ulrich Fischer 3. Prüfer: Prof. Dr. Rudolf Amann 4. Prüfer: PD Dr. Jens Harder Table of contents Summary 4 Zusammenfassung 6 Chapter I General introduction 8 The genus Pseudovibrio 9 Sponges and sponge-bacteria associations 13 Bacterial secretion systems and their role in symbiosis 16 Type III secretion system 16 Type VI secretion system 18 Oligotrophy in the oceans and bacterial adaptations 19 Phosphorus in oceanic environments 20 Phosphate limitation and the Pho regulon 23 Aim of the thesis 25 Chapter II The genus Pseudovibrio contains metabolically versatile and symbiotically interacting bacteria 34 Chapter III Isolation of facultatively oligotrophic bacteria 107 Chapter IV Pseudovibrio denitrificansT versus Pseudovibrio sp. FO-BEG1 – a comparison 121 Chapter V Response to phosphate limitation in Pseudovibrio sp. strain FO-BEG1 138 Chapter VI General conclusions 185 New aspects of the physiology of Pseudovibrio spp.-related strains 186 Pseudovibrio sp. FO-BEG1: a facultative symbiont of marine invertebrates 190 Phosphate starvation of Pseudovibrio sp. FO-BEG1 and implications for the environment 193 Pseudovibrio sp. strains FO-BEG1 and JE062 belong to the Pseudovibrio denitrificans species 200 Perspectives 201 Acknowledgments 210 Summary Bacteria belonging to the genus Pseudovibrio are frequently found in marine habitats, mainly in association with sponges, corals and tunicates. -
Expression Profiling Reveals Spot 42 Small RNA As a Key Regulator in The
Hansen et al. BMC Genomics 2012, 13:37 http://www.biomedcentral.com/1471-2164/13/37 RESEARCH ARTICLE Open Access Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida Geir Å Hansen1, Rafi Ahmad1,2, Erik Hjerde1, Christopher G Fenton3, Nils-Peder Willassen1,2 and Peik Haugen1,2* Abstract Background: Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria. One member of this family, Aliivibrio salmonicida, causes cold-water vibriosis in farmed Atlantic salmon. Its genome encodes Spot 42 with 84% identity to E. coli Spot 42. Results: We generated a A. salmonicida spf deletion mutant. We then used microarray and Northern blot analyses to monitor global effects on the transcriptome in order to provide insights into the biological roles of Spot 42 in this bacterium. In the presence of glucose, we found a surprisingly large number of ≥ 2X differentially expressed genes, and several major cellular processes were affected. A gene encoding a pirin-like protein showed an on/off expression pattern in the presence/absence of Spot 42, which suggests that Spot 42 plays a key regulatory role in the central metabolism by regulating the switch between fermentation and respiration. Interestingly, we discovered an sRNA named VSsrna24, which is encoded immediately downstream of spf. -
Innovations in Host and Microbial Sialic Acid Biosynthesis Revealed by Phylogenomic Prediction of Nonulosonic Acid Structure
Innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure Amanda L. Lewisa,b,1,2, Nolan Desaa, Elizabeth E. Hansenc, Yuriy A. Knireld, Jeffrey I. Gordonc, Pascal Gagneuxa,e, Victor Nizeta,b,f, and Ajit Varkia,e,g,1 aGlycobiology Research and Training Center, Departments of bPediatrics, gMedicine, and eCellular and Molecular Medicine, School of Medicine, and fSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093; dN.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 11991 Moscow, Russia; and cCenter for Genome Sciences, Washington University, St. Louis, MO 63108 Edited by Sen-itiroh Hakomori, Pacific Northwest Diabetes Research Institute, Seattle, WA, and approved June 19, 2009 (received for review March 9, 2009) Sialic acids (Sias) are nonulosonic acid (NulO) sugars prominently Sias are 9-carbon backbone derivatives of neuraminic (Neu) displayed on vertebrate cells and occasionally mimicked by bacte- and ketodeoxynonulosonic (Kdn) acids. They are actually part of rial pathogens using homologous biosynthetic pathways. It has a larger family of carbohydrate structures collectively called been suggested that Sias were an animal innovation and later nonulosonic acids (NulOs)‡. A number of NulO sugars other emerged in pathogens by convergent evolution or horizontal gene than Sias have been found in microbes, all of which are deriv- transfer. To better illuminate the evolutionary processes underly- atives of 4 isomeric 5,7-diamino-3,5,7,9-tetradeoxynon-2- ing the phenomenon of Sia molecular mimicry, we performed phy- ulosonic acids (12). At least 2 of these, the D-glycero-d-galacto logenomic analyses of biosynthetic pathways for Sias and related isomer [legionaminic acid (Leg)] (13, 14) and L-glycero-l-manno higher sugars derived from 5,7-diamino-3,5,7,9-tetradeoxynon-2- isomer [pseudaminic acid (Pse)] (15, 16), have striking structural ulosonic acids. -
Photobacterium
Diversification of Two Lineages of Symbiotic Photobacterium Henryk Urbanczyk1*, Yoshiko Urbanczyk1, Tetsuya Hayashi2,3, Yoshitoshi Ogura2,3 1 Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan, 2 Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan, 3 Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan Abstract Understanding of processes driving bacterial speciation requires examination of closely related, recently diversified lineages. To gain an insight into diversification of bacteria, we conducted comparative genomic analysis of two lineages of bioluminescent symbionts, Photobacterium leiognathi and ‘P. mandapamensis’. The two lineages are evolutionary and ecologically closely related. Based on the methods used in bacterial taxonomy for classification of new species (DNA-DNA hybridization and ANI), genetic relatedness of the two lineages is at a cut-off point for species delineation. In this study, we obtained the whole genome sequence of a representative P. leiognathi strain lrivu.4.1, and compared it to the whole genome sequence of ‘P. mandapamensis’ svers.1.1. Results of the comparative genomic analysis suggest that P. leiognathi has a more plastic genome and acquired genes horizontally more frequently than ‘P. mandapamensis’. We predict that different rates of recombination and gene acquisition contributed to diversification of the two lineages. Analysis of lineage- specific sequences in 25 strains of P. leiognathi and ‘P. mandapamensis’ found no evidence that bioluminescent symbioses with specific host animals have played a role in diversification of the two lineages. Citation: Urbanczyk H, Urbanczyk Y, Hayashi T, Ogura Y (2013) Diversification of Two Lineages of Symbiotic Photobacterium.