Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches
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Adaptive Introgression Between Anopheles Sibling Species Eliminates a Major Genomic Island but Not Reproductive Isolation
ARTICLE Received 22 Feb 2014 | Accepted 28 May 2014 | Published 25 Jun 2014 DOI: 10.1038/ncomms5248 OPEN Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation Chris S. Clarkson1,*, David Weetman1,*, John Essandoh1,2, Alexander E. Yawson2,3, Gareth Maslen4, Magnus Manske4, Stuart G. Field5, Mark Webster6, Tiago Anta˜o1, Bronwyn MacInnis4, Dominic Kwiatkowski4,7 & Martin J. Donnelly1,4 Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (B1.5% of the genome) between species. Despite this massive dis- ruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation. 1 Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK. 2 Cape Coast Department of Entomology and Wildlife, School of Biological Science, University of Cape Coast, Cape Coast, Ghana. 3 Biotechnology and Nuclear Agriculture Research Institute, Ghana Atomic Energy Commission, PO Box LG 80, Legon, Accra, Ghana. -
Mobile Genetic Elements in Streptococci
Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G. -
Proquest Dissertations
Automated learning of protein involvement in pathogenesis using integrated queries Eithon Cadag A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2009 Program Authorized to Offer Degree: Department of Medical Education and Biomedical Informatics UMI Number: 3394276 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI Dissertation Publishing UMI 3394276 Copyright 2010 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. uest ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 University of Washington Graduate School This is to certify that I have examined this copy of a doctoral dissertation by Eithon Cadag and have found that it is complete and satisfactory in all respects, and that any and all revisions required by the final examining committee have been made. Chair of the Supervisory Committee: Reading Committee: (SjLt KJ. £U*t~ Peter Tgffczy-Hornoch In presenting this dissertation in partial fulfillment of the requirements for the doctoral degree at the University of Washington, I agree that the Library shall make its copies freely available for inspection. I further agree that extensive copying of this dissertation is allowable only for scholarly purposes, consistent with "fair use" as prescribed in the U.S. -
Divergence of a Genomic Island Leads to the Evolution of Melanization in a Halophyte Root Fungus
The ISME Journal https://doi.org/10.1038/s41396-021-01023-8 ARTICLE Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus 1,2 3 4 5,6 7,8,9 Zhilin Yuan ● Irina S. Druzhinina ● John G. Gibbons ● Zhenhui Zhong ● Yves Van de Peer ● 10 11 2 1,2 12 13 Russell J. Rodriguez ● Zhongjian Liu ● Xinyu Wang ● Huanshen Wei ● Qi Wu ● Jieyu Wang ● 12 3 1,2 14,15 Guohui Shi ● Feng Cai ● Long Peng ● Francis M. Martin Received: 7 October 2020 / Revised: 9 May 2021 / Accepted: 24 May 2021 © The Author(s) 2021. This article is published with open access, corrected publication 2021 Abstract Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number 1234567890();,: 1234567890();,: variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. -
The Pathogenomics and Evolution of Anthrax-Like Bacillus Cereus Isolates and Plasmids
The Pathogenomics and Evolution of Anthrax-like Bacillus cereus Isolates and Plasmids A white paper proposal submitted by: Geraldine A. Van der Auwera, Ph.D. Harvard Medical School Michael Feldgarden, Ph.D. Genomic Sequencing Center for Infectious Diseases The Broad Institute of MIT and Harvard 1 Executive summary A key member of the Bacillus cereus group, Bacillus anthracis is defined by phenotypic and molecular characteristics that are conferred by two large plasmids, pXO1 and pXO2. However the very concept of B. anthracis as a distinct species has been called into question by recent discoveries of “intermediate” isolates identified as B. cereus and B. thuringiensis but possessing features similar to those of B. anthracis, including large plasmids that share a common backbone with pXO1 and/or pXO2. Many of these “intermediate” isolates possess potential or demonstrated lethal pathogenic properties and are sometimes called “anthrax-like”, even though they do not meet the strict definition of anthrax-causing B. anthracis. We recently showed that pXO1- and pXO2- like plasmids are widely prevalent in environmental isolates of the B. cereus group. Because B. anthracis-like isolates do not possess all the molecular hallmarks of typical B. anthracis, there is a significant risk that they would escape being flagged as dangerous. Consequently, accidental infection by naturally occurring pathotypes which are not immediately recognized as life-threatening could present a serious health concern. Such cases have already been reported, some with a fatal outcome. The second risk posed by these B. anthracis-like isolates could be the intentional use as “stealth anthrax” bioweapon, either in natural form or with genetic modifications that would require only minimal skills and facilities to produce. -
QUANTIFYING TRENDS in BACTERIAL VIRULENCE and PATHOGEN-ASSOCIATED GENES THROUGH LARGE SCALE BIOINFORMATICS ANALYSIS By
QUANTIFYING TRENDS IN BACTERIAL VIRULENCE AND PATHOGEN-ASSOCIATED GENES THROUGH LARGE SCALE BIOINFORMATICS ANALYSIS by Anastasia Amber Fedynak B.Comp., University of Guelph, 2003 B.Sc., University of Alberta, 2002 THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY In the Department of Molecular Biology and Biochemistry © Anastasia Fedynak 2007 SIMON FRASER UNIVERSITY 2007 All rights reserved. This work may not be reproduced in whole or in part, by photocopy or other means, without permission of the author. APPROVAL Name: Anastasia Amber Fedynak Degree: Doctor of Philosophy Title of Thesis: Quantifying trends in bacterial virulence and pathogen-associated genes through large scale bioinformatics analysis Examining Committee: Chair: Dr. Bruce P. Brandhorst Professor, Department of Molecular Biology and Biochemistry Dr. Fiona S.L. Brinkman Senior Supervisor Associate Professor, Department of Molecular Biology and Biochemistry Dr. Lisa Craig Supervisor Assistant Professor, Department of Molecular Biology and Biochemistry Dr. Kay C. Wiese Supervisor Associate Professor, School of Computing Science Dr. Jack Chen Internal Examiner Associate Professor, Department of Molecular Biology and Biochemistry Dr. Gee W. Lau External Examiner Assistant Professor, College of Veterinary Medicine, University of Illinois at Urbana-Champaign Date Defended: Monday December 10, 2007 ii SIMON FRASER UNIVERSITY LIBRARY Declaration of Partial Copyright Licence The author, whose copyright is declared on the title page of this work, has granted to Simon Fraser University the right to lend this thesis, project or extended essay to users of the Simon Fraser University Library, and to make partial or single copies only for such users or in response to a request from the library of any other university, or other educational institution, on its own behalf or for one of its users. -
Helicobacter Pylori Infection Causes Characteristic DNA Damage Patterns in Human Cells
Report Helicobacter pylori Infection Causes Characteristic DNA Damage Patterns in Human Cells Graphical Abstract Authors Max Koeppel, Fernando Garcia-Alcalde, Frithjof Glowinski, Philipp Schlaermann, Thomas F. Meyer Correspondence [email protected] In Brief The gastric pathogen H. pylori can cause cancer in humans by compromising the genomic integrity of infected cells. Koeppel et al. show that infection affects the DNA damage response and reveal a DNA damage pattern reminiscent of genomic aberrations found in gastric tumors. Highlights Accession Numbers d H. pylori impairs the DNA repair response in normal human GSE55699 epithelial cells d Distinct genomic regions show increased susceptibility to H. pylori-induced damage d DNA damage accumulates in telomere-proximal, actively transcribed regions d Susceptible genomic regions overlap with gastric cancer genomic aberrations Koeppel et al., 2015, Cell Reports 11, 1703–1713 June 23, 2015 ª2015 The Authors http://dx.doi.org/10.1016/j.celrep.2015.05.030 Cell Reports Report Helicobacter pylori Infection Causes Characteristic DNA Damage Patterns in Human Cells Max Koeppel,1 Fernando Garcia-Alcalde,1 Frithjof Glowinski,1 Philipp Schlaermann,1 and Thomas F. Meyer1,* 1Department of Molecular Biology, Max Planck Institute for Infection Biology, Charite´ platz 1, 10117 Berlin, Germany *Correspondence: [email protected] http://dx.doi.org/10.1016/j.celrep.2015.05.030 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). SUMMARY (Jenks et al., 2003; Touati et al., 2003). This process has been linked to reduced expression of mismatch repair genes (Kim Infection with the human pathogen Helicobacter et al., 2002) and increased expression of activation-induced cyti- pylori (H. -
Estimation of Pathogenic Potential of an Environmental Pseudomonas
www.nature.com/scientificreports OPEN Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics Carola Berger1, Christian Rückert2, Jochen Blom3, Korneel Rabaey4, Jörn Kalinowski2 & Miriam A. Rosenbaum1,5* The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defned and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using diferent genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential. Pseudomonas aeruginosa has been isolated from terrestrial and marine soil, fresh and salt water, sewage, plants, animals, and humans 1. For the latter habitats, it is known as an opportunistic pathogen, which usually spreads to already vulnerable patients, causing ~ 10% of all nosocomial infections in most European Union hospitals2. -
Bacterial Genetics
BACTERIAL GENETICS Genetics is the study of genes including the structure of genetic materials, what information is stored in the genes, how the genes are expressed and how the genetic information is transferred. Genetics is also the study of heredity and variation. The arrangement of genes within organisms is its genotype and the physical characteristics an organism based on its genotype and the interaction with its environment, make up its phenotype. The order of DNA bases constitutes the bacterium's genotype. A particular organism may possess alternate forms of some genes. Such alternate forms of genes are referred to as alleles. The cell's genome is stored in chromosomes, which are chains of double stranded DNA. Genes are sequences of nucleotides within DNA that code for functional proteins. The genetic material of bacteria and plasmids is DNA. The two essential functions of genetic material are replication and expression. Structure of DNA The DNA molecule is composed of two chains of nucleotides wound around each other in the form of “double helix”. Double-stranded DNA is helical, and the two strands in the helix are antiparallel. The backbone of each strand comprises of repeating units of deoxyribose and phosphate residue. Attached to the deoxyribose is purine (AG) or pyrimidine (CT) base. Nucleic acids are large polymers consisting of repeating nucleotide units. Each nucleotide contains one phosphate group, one deoxyribose sugar, and one purine or pyrimidine base. In DNA the sugar is deoxyribose; in RNA the sugar is ribose. The double helix is stabilized by hydrogen bonds between purine and pyrimidine bases on the opposite strands. -
Comprehensive Analysis of Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools
bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. 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 Comprehensive analysis of mobile genetic elements in the gut microbiome 2 reveals phylum-level niche-adaptive gene pools 3 Xiaofang Jiang1,2,†, Andrew Brantley Hall2,3,†, Ramnik J. Xavier1,2,3,4, and Eric Alm1,2,5,* 4 1 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, 5 Cambridge, MA 02139, USA 6 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 7 3 Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard 8 Medical School, Boston, MA 02114, USA 9 4 Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General 10 Hospital and Harvard Medical School, Boston, MA 02114, USA 11 5 MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 12 02142, USA 13 † Co-first Authors 14 * Corresponding Author bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. 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. 15 Abstract 16 Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer 17 could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could 18 threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological 19 importance and medical relevance, MGEs from the gut microbiome have not been systematically 20 characterized. -
14S802 - Strain Specific Pathogenicity of Staphylococcus Aureus Final Report
14S802 - Strain Specific Pathogenicity of Staphylococcus aureus Final Report This project was funded under the Department of Agriculture, Food and the Marine Competitive Funding Programme. SUMMARY Mastitis is a costly endemic disease for the dairy industry. It is primarily caused by bacterial infection and is the most common reason for antibiotic use in dairy cows in Ireland. Staphylococcus aureus is the most common mastitis pathogen in Ireland and the S. aureus strains that cause mastitis belong to specific bovine-adapted lineages. Current selection for mastitis-resistance is based on the host immune response, as determined by somatic cell count (SCC). However, the ability of S. aureus to evade and subvert the host immune response is well known, including the ability to internalise and survive within host cells. This project tested the hypothesis that bovine intramammary infection with different S. aureus strains results in differential activation of the host immune response. Supporting this hypothesis, significant differences between S. aureus lineages in their ability to internalise within bovine mammary epithelial cells were found with some strains internalising at higher levels than others. It was also found that some strains induced higher expression of cytokines and chemokines responsible for attracting immune cells and these strains induced mammary epithelial cells to produce factors that attracted somatic cells, while other strains did not. Differences in disease presentation in vivo in cows infected with different strains were also observed, indicating strain-specific virulence. Significantly higher somatic cell count and anti- Staphylococcus IgG and significantly lower milk yield were observed in response to infection with a more virulent strain. -
The Role of Genomics in the Identification, Prediction, and Prevention of Biological Threats
Perspective The Role of Genomics in the Identification, Prediction, and Prevention of Biological Threats W. Florian Fricke, David A. Rasko, Jacques Ravel* Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, Maryland, United States of America Since the publication in 1995 of the first Biodefense Funding for of programs, the genome sequences of over complete genome sequence of a free-living Genomic Research 90,000 influenza viruses were rapidly organism, the bacterium Haemophilus influ- generated and are now deposited in enzae [1], more than 1,000 genomes of Since the anthrax letter attacks of 2001, GenBank (http://www.ncbi.nlm.nih.gov/ species from all three domains of life— when letters containing anthrax spores genomes/FLU/aboutdatabase.html). Be- Bacteria, Archaea, and Eukarya—have were mailed to several news media offices cause of the availability of large sequencing been completed and a staggering 4,300 and two Democratic senators in the capacity and the large amount of informa- are in progress (not including an even United States, killing five people and tion, the response to the 2009 H1N1 larger number of viral genome projects) infecting 17 others, funding agencies in influenza pandemic was rapid and efficient (GOLD, Genomes Online Database v. the US and other countries have priori- (Box 2): Genomics information was gener- 2.0; http://www.genomesonline.org/gold. tized research projects on organisms that ated within days and validated diagnostic cgi, as of August 2009). Whole-genome might potentially challenge our security tools were approved within weeks [5,6]. A shotgun sequencing remains the standard and economy should they be used as global response was made possible through in biomedical, biotechnological, environ- biological weapons.