Topic: Genetic Recombination in Bacteria B.Sc. Botany (Hons.) I Group: C Dr
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
Section 4. Guidance Document on Horizontal Gene Transfer Between Bacteria
306 - PART 2. DOCUMENTS ON MICRO-ORGANISMS Section 4. Guidance document on horizontal gene transfer between bacteria 1. Introduction Horizontal gene transfer (HGT) 1 refers to the stable transfer of genetic material from one organism to another without reproduction. The significance of horizontal gene transfer was first recognised when evidence was found for ‘infectious heredity’ of multiple antibiotic resistance to pathogens (Watanabe, 1963). The assumed importance of HGT has changed several times (Doolittle et al., 2003) but there is general agreement now that HGT is a major, if not the dominant, force in bacterial evolution. Massive gene exchanges in completely sequenced genomes were discovered by deviant composition, anomalous phylogenetic distribution, great similarity of genes from distantly related species, and incongruent phylogenetic trees (Ochman et al., 2000; Koonin et al., 2001; Jain et al., 2002; Doolittle et al., 2003; Kurland et al., 2003; Philippe and Douady, 2003). There is also much evidence now for HGT by mobile genetic elements (MGEs) being an ongoing process that plays a primary role in the ecological adaptation of prokaryotes. Well documented is the example of the dissemination of antibiotic resistance genes by HGT that allowed bacterial populations to rapidly adapt to a strong selective pressure by agronomically and medically used antibiotics (Tschäpe, 1994; Witte, 1998; Mazel and Davies, 1999). MGEs shape bacterial genomes, promote intra-species variability and distribute genes between distantly related bacterial genera. Horizontal gene transfer (HGT) between bacteria is driven by three major processes: transformation (the uptake of free DNA), transduction (gene transfer mediated by bacteriophages) and conjugation (gene transfer by means of plasmids or conjugative and integrated elements). -
The Obscure World of Integrative and Mobilizable Elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget
The obscure world of integrative and mobilizable elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget To cite this version: Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget. The obscure world of integrative and mobilizable elements: Highly widespread elements that pirate bacterial conjugative systems. Genes, MDPI, 2017, 8 (11), pp.337. 10.3390/genes8110337. hal- 01686871 HAL Id: hal-01686871 https://hal.archives-ouvertes.fr/hal-01686871 Submitted on 26 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License G C A T T A C G G C A T genes Review The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems Gérard Guédon *, Virginie Libante, Charles Coluzzi, Sophie Payot and Nathalie Leblond-Bourget * ID DynAMic, Université de Lorraine, INRA, 54506 Vandœuvre-lès-Nancy, France; [email protected] (V.L.); [email protected] (C.C.); [email protected] (S.P.) * Correspondence: [email protected] (G.G.); [email protected] (N.L.-B.); Tel.: +33-037-274-5142 (G.G.); +33-037-274-5146 (N.L.-B.) Received: 12 October 2017; Accepted: 15 November 2017; Published: 22 November 2017 Abstract: Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. -
Transformation and Homologous Recombination in Mycoplasma Gallisepticum Jian Jian Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1-1-1993 Transformation and homologous recombination in Mycoplasma gallisepticum Jian Jian Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Recommended Citation Jian, Jian, "Transformation and homologous recombination in Mycoplasma gallisepticum" (1993). Retrospective Theses and Dissertations. 18012. https://lib.dr.iastate.edu/rtd/18012 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Transformation and homologous recombination in Mycoplasma gallisepticum by Jian Cao A Thesis Submitted to the Graduate Faculty in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE Department: Microbiology, Immunology and Preventive Medicine Major: Veterinary Microbiology "-- ... - .. - -J . Signatures have been redacted for privacy Iowa State University Ames, Iowa 1993 II TABLE OF CONTENTS LIST OF TABLES iv LIST OF FIGURES v LIST OF ABBREVIATIONS vi ACKNOWLEDGMENTS vii INTRODUCTION General Characteristics of Mycoplasmas Antigenic variation 1 Virulence factors 3 Chromosomal structure 4 Physical and genetic maps 4 Nucleotide composition and codon usage 5 Transformation and transposition -
Genetic Exchange in Bacteria
Systems Microbiology Monday Oct 16 - Ch 10 -Brock Genetic Exchange in Bacteria •• HomologousHomologous recombinationrecombination •• TransformationTransformation •• PlasmidsPlasmids andand conjugationconjugation •• TransposableTransposable elementselements •• TransductionTransduction (virus(virus mediatedmediated xchangexchange)) Gene exchange in bacteria • Transfer of DNA from one bacterium to another is a common means of gene dispersal. It has a big effect on bacterial evolution, and tremendous practical implications. For example, lateral transfer is responsible for the spread drug resistance determinants between bacterial species. • Three common mechanisms of lateral gene exchange : – Transformation (extracellular DNA uptake) – Conjugation (bacterial mating systems) – Transduction (viral mediated gene exchange) RecA mediated Homologous recombination Images removed due to copyright restrictions. See Figures 10-9 and 10-10 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms.11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291. Gene exchange in bacteriaTransformation The Griffith Experiment S Injection Dead mouse; • Discovered by Griffith in yields S1 cells 1928 during the course of his Live "smooth" (encapsulated) studies of virulence in type 1 pneumococci (S1) Streptococcus pneumoniae. Dead S Live mouse Heat-killed S1 • S=smooth colony Live mouse morphotype Live "rough" (unencapsulated) pneumococci (R1 or R2) derived by subculture from S1 or S2, respectively • R=rough colony Dead mouse; yields S cells morphotype R1 + Dead S + 1 Live R1 Killed S1 R2 + Dead S + Dead mouse; yields S1 cells Live R2 Killed S2 Figure by MIT OCW. Gene exchange mechanisms in bacteria Transformation The Griffith Experiment Injection Dead mouse; S yields S cells Avery, MacLeod, and McCarthy (1944) 1 fractionation studies led to conclusion that Live "smooth" (encapsulated) type 1 pneumococci (S ) transformation principle is DNA. -
Recombination of Escherzchza Colz and Bacteriophage Lambda
Symposium on Genetic Exchange : XIlI Internaiionul Congress of Genetics PROGRESS TOWARD A METABOLIC INTERPRETATION OF GENETIC RECOMBINATION OF ESCHERZCHZA COLZ AND BACTERIOPHAGE LAMBDA ALVIN J. CLARK Department of Molecular Biology, University of California, Berkeley, California 94720 is a metabolically active cellular component of bacteria. Transcrip- DNA tion and replication can proceed continuously throughout the growth and division of bacterial cells. Enzymes methylate DNA bases and when they have not acted restriction enzymes nick and break double-stranded DNA mole- cules producing substrates for further degradation. When radiations or chemicals damage DNA, repair enzymes either change or remove damaged portions, restor- ing the DNA to its original state, or they deal with secondary lesions produced by faulty metabolism of the unremoved primary lesions. In addition to these realms of DNA metabolism there is the realm of genetic recombination. A metabolic interpretation of genetic recombination will require knowledge of the structures of the starting materials and end products of recom- bination. It will also require a list of the enzymes or proteins catalyzing the steps in recombination together with their activities and substrate specificities and ultimately the intermediates and products of each step. Furthermore E! metabolic interpretation will require a knowledge of the regulation of the synthesis and activities of the enzymes and other proteins of recombination. Finally the rela- tionships between recombination and the other realms of DNA metabolism must be stated as a list of common and unique intermediates and enzymes. At present we are far from such a metabolic interpretation although consider- able progress has been made. In the present report I shall emphasize work per- formed in my own laboratory on the recombination of E. -
Lab Exercise 15: Bacterial Conjugation
Microbiology BIOL 275 BACTERIAL CONJUGATION I. OBJECTIVES • To demonstrate the technical procedure to monitor the conjugational transfer of genetic material from one cell to another. • To learn about the various genetic elements involved in bacterial sex and recombination events. • To recognize and discuss the advantages and limitations of the conjugational procedure in genetic recombination experiments. II. INTRODUCTION There are three different mechanisms for genetic exchange between bacteria: conjugation, transformation and transduction. Conjugation has been shown to occur in many bacterial species especially the Gram negative organisms. In Enterobacteriaceae (Escherichia, Salmonella, Shigella, Vibrio, etc.), the transfer has been shown to cross the taxonomic lines with varying rates of efficiency. Thus, conjugation has become a tool to study the location and function of many genes, including genes responsible for virulence, antibiotic resistance, metabolic functions, regulatory proteins, phage attachment sites, etc. E. coli has been the model organism in conjugation studies. It may become infected with an extrachromosomal genetic element (a plasmid called the F factor) which mediates certain events such as the synthesis of a pilus (the F or sex pilus), and the rapid infection of all susceptible bacteria with this F factor. The pilus has been shown to facilitate attachment of the male (or F+ cells) to the female (or F- cells) which do not contain the F factor. It was previously thought that the hollow center of the pilus constituted a passageway for the F factor to be transferred to the female. However, recent evidence suggests that the pilus may be used as a "hook" to bring the two cells close together and that the DNA transfer actually occurs outside the pilus. -
Bacterial Conjugation
16 Mechanisms of Genetic Variation 1 16.1 Mutations 1. Distinguish spontaneous from induced mutations, and list the most common ways each arises 2. Construct a table, concept map, or picture to summarize how base analogues, DNA-modifying agents, and intercalating agents cause mutations 3. Discuss the possible effects of mutations 2 Mutations: Their Chemical Basis and Effects • Stable, heritable changes in sequence of bases in DNA – point mutations most common • from alteration of single pairs of nucleotide • from the addition or deletion of nucleotide pairs – larger mutations are less common • insertions, deletions, inversions, duplication, and translocations of nucleotide sequences • Mutations can be spontaneous or induced 3 16.4 Creating Additional Genetic Variability 1. Describe in general terms how recombinant eukaryotic organisms arise 2. Distinguish vertical gene transfer from horizontal gene transfer 3. Summarize the four possible outcomes of horizontal gene transfer 4. Compare and contrast homologous recombination and site-specific recombination 4 Creating Additional Genetic Variability • Mutations are subject to selective pressure – each mutant form that survives becomes an allele, an alternate form of a gene • Recombination is the process in which one or more nucleic acids are rearranged or combined to produce a new nucleotide sequence (recombinants) 5 Sexual Reproduction and Genetic Variability • Vertical gene transfer = transfer of genes from parents to progeny • In eukaryotes – sexual reproduction is accompanied by genetic -
Impact of Transgenic Technologies on Functional Genomics 75
Curr. Issues Mol. Biol. (2003) 5: 75-98. Impact of Transgenic Technologies on Functional Genomics 75 Impact of Transgenic Technologies on Functional Genomics Cooduvalli S. Shashikant1* and Frank H. Ruddle2 biotechnological capabilities. Twentieth century genetics was dominated by the idea 1 Dept. Dairy and Animal Science, College of Agricultural of introducing exogenous genetic material into the genome Sciences, 324 Henning, University Park, PA 16802, USA of experimental organisms. The foundation of bacterial 2 Depts of MCDB and Genetics, Yale University, New genetics lies in the discovery of transformation, conjugation Haven, CT 06511, USA and transduction. A combination of bacterial gene transfer technologies and molecular biology tools resulted in the birth of recombinant DNA technology in the seventies. The Abstract progress made in bacterial genetics inspired development of similar methods to study mammalian genetics. Here, Gene transfer technologies in mammals are the focus mammalian gene transfer technology is broadly considered of renewed interest owing to the recent emphasis on under three technological breakthroughs achieved during analyzing gene function in the postgenomic era. Three the past two decades: (a) transgenic technology; (b) gene important developments in this area include targeting; and (c) nuclear transfer or ‘cloning’. In this review, transgenics, gene targeting and nuclear transfer or we describe the emergence of these technologies and animal cloning. These technological innovations have current advances in the analysis of mammalian gene enhanced our ability to analyze gene function at the function. level of the whole organism and have provided the means to modify gene expression. This review Historical Perspective discusses the origins and current status of transgenic technologies. -
Double-Strand End Repair Via the Recbc Pathway in Escherichia Coli Primes DNA Replication
Downloaded from genesdev.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press Double-strand end repair via the RecBC pathway in Escherichia coli primes DNA replication Andrei Kuzminov1 and Franklin W. Stahl Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229 USA To study the relationship between homologous recombination and DNA replication in Escherichia coli,we monitored the behavior of phage chromosomes, repressed or not for gene activities. Recombination in our system is stimulated both by DNA replication and by experimentally introduced double-strand ends, supporting the idea that DNA replication generates occasional double-strand ends. We report that the RecBC recombinational pathway of E. coli uses double-strand ends to prime DNA synthesis, implying a circular relationship between DNA replication and recombination and suggesting that the primary role of recombination is in the repair of disintegrated replication forks arising during vegetative reproduction. [Key Words: DSB repair; homologous recombination; DNA replication; recA; recD; recBC] Received October 15, 1998; revised version accepted December 22, 1998. Homologous recombination was first seen as the cross- 1998). soon emerged as a promising system, following ing-over of chromosomes in cells undergoing meiosis. the finding that it has homologous recombination (Jacob The first scheme of crossing-over (Janssens 1909) was of and Wollman 1954; Kaiser 1955) and that its growth is the break–join type, according to which homologous only partly dependent on recombination (Manly et al. chromosomes would break at the same position and 1969; Enquist and Skalka 1973). The experiments of Me- swap arms (Fig. 1). The copy-choice scheme (Belling selson and Weigle showed the presence of parental DNA 1931a, b) was the first to link homologous recombina- in recombinants, ruling out copy–choice as the only tion with chromosomal replication (Fig. -
Joshua Lederberg on Bacterial Recombination
| CLASSIC Joshua Lederberg on Bacterial Recombination Mark Johnston1 Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045 ORCID ID: 0000-0002-4932-7229 (M.J.) ORIGINAL CITATION Gene Recombination and Linked Segregations in Escherichia coli Joshua Lederberg GENETICS September 1, 1947 32: 505–525 his paper describes the first genetic analysis of bacteria. Lederberg decided to take a different tack. Instead of trying TBefore its publication, most scientists wondered if bacteria to replicate DNA transformation in an existing model organ- even had genes. Many thought bacteria to be a distinct form ism, why not establish a new system for genetic analysis of of life, separate from higher organisms like Drosophila bacteria? The conventional wisdom was that bacteria do not and maize, which were known to follow Mendel’s principles engage in sex, which would make standard genetic analysis of heredity. But when George Beadle and Edward Tatum impossible. There had been a few attempts to detect genetic showed in 1941 that Neurospora obeys Mendel’slaws(Beadle exchange in bacteria, but the results were inconclusive. Lederberg and Tatum 1941), and 2 years later Salvador Luria and Max decided to give it another try. Why not? He knew he had Delbrück reported in GENETICS that bacterial mutations arise nothing to lose: he did not need to complete a research project at random (Murray 2016), microorganisms began to shed their to receive his MD degree. outsider status. Then, when Avery, McLeod, and McCarty iden- Lederberg chose to use Escherichia coli for these experi- tified DNA as the substance that stably converts one form of ments and started the painstaking process of mutagenizing Pneumococcus bacteria to another (Avery et al. -
Bacterial Genetics
BACTERIAL GENETICS (Mutation & Recombination) RAKESH SHARDA Department of Veterinary Microbiology NDVSU College of Veterinary Science & A.H., MHOW BACTERIAL MUTATION Mutation • A heritable change in the nucleotide sequence of a gene is called a mutation. • Mutations are usually detrimental, but they can also lead to beneficial changes. • A mutant is called an auxotroph if the mutation leads to a new nutrient requirement, while the wild type strain is known as prototroph. Mutation • Two types – spontaneous and induced – Spontaneous mutation occurs naturally, about one in every million to one in every billion divisions, and is probably due to low level natural mutagens present in the environment. – Induced mutation is caused by mutagens that cause a much higher rate of mutation; induced by chemicals or radiations • Other mutations are caused by transposable genetic element Chemical mutagens • chemical modifications of purine and pyrimidine bases that alter their hydrogen-bonding properties, e.g. nitrous acid converts cytosine to uracil which then forms hydrogen bonds with adenine rather than guanine. • incorporation of base analogs (compounds that chemically resemble a nucleotide base closely, but do not have the hydrogen-bonding properties of the natural base ) during DNA replication in place of the natural base, e.g. 2-amino purine, a compound that resembles adenine, and 5-bromouracil, a compound that resembles thymine. • intercalating agents (planar three-ringed molecules that are about the same size as a nucleotide base pair) can insert or intercalate between adjacent base pairs during DNA replication thus pushing the nucleotides far enough apart so that an extra nucleotide is often added to the growing chain during DNA replication, e.g.