DOCSLIB.ORG

Soil Bacterial Populations Are Shaped by Recombination and Gene-Specific

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Soil Bacterial Populations Are Shaped by Recombination and Gene-Specific The ISME Journal (2020) 14:1834–1846 https://doi.org/10.1038/s41396-020-0655-x ARTICLE Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow 1 2 2 2 Alexander Crits-Christoph ● Matthew R. Olm ● Spencer Diamond ● Keith Bouma-Gregson ● Jillian F. Banfield 2,3,4,5 Received: 17 September 2019 / Revised: 22 March 2020 / Accepted: 2 April 2020 / Published online: 23 April 2020 © The Author(s) 2020. This article is published with open access Abstract Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species. The relative impacts of clonal interference, gene-specific selection, and recombination in many abundant but rarely cultivated soil microbes remain unknown. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic inferences about population structure are made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in each population. Genomic nucleotide fi 1234567890();,: 1234567890();,: identity of assembled genomes was signi cantly associated with local geography for over half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in metabolite biosynthesis and extracellular transport were characterized by elevated nucleotide diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7–36% of loci genome-wide. Within multiple populations we identified genes with unusually high spatial differentiation of alleles, fewer recombinant events, elevated ratios of nonsynonymous to synonymous variants, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape genetic variation in several understudied soil bacterial lineages. Introduction Soil microbial communities play key biogeochemical roles in terrestrial ecosystems [1]. Within a single hectare of temperate grassland soil, there can be over 1000 kg of microbial biomass and corresponding large microbial Supplementary information The online version of this article (https:// doi.org/10.1038/s41396-020-0655-x) contains supplementary population sizes [2]. Recent progress has been made in material, which is available to authorized users. cataloging the diversity of 16S rRNA genes in soils [3], which is useful for understanding microbial community * fi Jillian F. Ban eld composition, but this technique is incapable of discerning jbanfi[email protected] most genetic variation within populations [4]. In addition, 1 Department of Plant and Microbial Biology, University of many of the most common soil microorganisms, such as the California, Berkeley, CA, USA highly abundant Acidobacteria, Verrucomicrobia, and 2 Department of Earth and Planetary Science, University of Gemmatimonadetes phyla, are underrepresented in or nearly California, Berkeley, CA, USA absent from culture collections and genomic databases, 3 Department of Environmental Science, Policy, and Management, even at the level of class or phylum [1, 5, 6]. For these University of California, Berkeley, CA, USA reasons, the processes of recombination and selection in 4 Earth Sciences Division, Lawrence Berkeley National Laboratory, many of the most globally prolific soil microbial phyla Berkeley, CA, USA remain unstudied. However, genome-resolved metage- 5 Chan Zuckerberg Biohub, San Francisco, CA, USA nomics, in which shotgun sequencing of metagenomic Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland. 1835 DNA is assembled and binned into draft genomes, has [27, 28]. In soil microbial populations, comparative fre- recently resulted in whole genome characterization of these quencies of gene-specific sweeps versus genome-wide clo- rarely cultivated but widespread soil bacteria [7–11]. nal strain competition and replacement are largely Sequence variation within genome-resolved metagenomic unknown, as are the spatial scales at which these evolu- datasets can therefore be used to track changes in allele tionary processes can occur. frequencies, and to infer the operation of evolutionary for- Previously, we conducted a large scale genome-resolved ces of genetic drift, natural selection, and homologous metagenomics study of soils from a grassland meadow in recombination in these natural populations [12, 13]. the Angelo Coast Range Reserve in northern California that Homologous recombination can vary dramatically in its established a dataset of 896 phylogenetically diverse importance relative to the other processes for different microbial genomes dereplicated by species, and reported on microbial species. Analyses of reference genomes have community composition [29]. The soil at the site is a sandy shown that homologous recombination frequently occurs in loam mixture of ~45% clay-, ~45% silt-, and 10% sand- bacteria populations, both globally and locally [14–16]. For sized particles [8], with pH values in the range of 4.6–4.9. example, certain populations of hotspring Cyanobacteria The mineralogy of the soils at the site was previously found approach panmixia, where recombination is so frequent that to be predominantly vermiculite, with plagioclase and alkali individual cells are unlinked random mixtures of alleles feldspars and minor apatite [30]. The soils were classified as [17]. In other species-like oceanic Vibrio, recombination is Ultic Haploxeralfs of the Holohan-Hollowtree-Casabonne high but large blocks of alleles important for ecological complex, and at a depth of 30 cm were found to have a bulk niche differentiation are co-inherited and may remain linked density of ~2.0 g/cm3, a cation exchange capacity between due to selection [18, 19]. In soils, Streptomyces flavogriseus 17 and 19 meq per 100 g soil, C:N ratios from 10–12, and isolates were also found to approach a freely recombining total C concentrations of 10 mg g−1 up to 18 mg g−1 [30]. panmixia [20]. In contrast, Myxoccocus xanthus isolates The grassland is dominated by annual Mediterranean recovered from a series of soil samples were distinct but grasses and forbs [8, 31]. The meadow has been part of a highly clonal, implying recombination between strains was rainfall amendment climate change study ongoing for over low [21]. However, despite their frequent cultivation, 17 years and has also been studied in the context of plant cultivation-independent studies show that those taxa are diversity and productivity [32], invertebrate herbivores and comparatively rare in soils compared with undercultivated predators [31], fungal communities [33], soil organic matter members of the Acidobacteria, Gemmatimonadetes, and [30], metabolomics, and metaproteomics [8]. By analyzing Verrucomicrobia [1]. The degree of recombination in these the population genomics of 19 highly abundant bacterial rarely cultivated but abundant soil bacterial lineages has not species across this meadow, we found high nucleotide been investigated, but recombination may be widespread, as diversity within samples, intrapopulation genetic structure high cell densities could promote the sharing of genetic often shifting over local spatial scales, varying degrees of material via transformation [22], conjugation [23], or the homologous recombination for different species, and gene- uptake of extracellular vesicles [24]. specific population differentiation partially driven by When recombination rates are low or selection is extre- selection. mely strong, several clonal strains compete until one or more beneficial alleles is highly selected for, resulting in a single clonal genotype increasing in abundance or even Materials and methods sweeping to fixation. However, when recombination unlinks gene variants within a population, beneficial alleles Sampling, genome sequencing, and metagenomic can sweep through a population independent of genomic assembly context in a selective sweep [25] with gene/locus-specific effects. One genome-resolved metagenomic study observed The sampling scheme, local soil characteristics, and study a single clonal sweep over a 9 year period for one Chlor- design that were utilized in this analysis have been pre- obium population in a freshwater lake [26], while most of viously described [29]. Previously, 60 soil samples were the other bacterial populations studied possessed genomic collected at depths of 10–20, 20–30, and 30–40 cm near the loci with unusually few SNPs (single nucleotide poly- respective centers of six 10 m diameter plots, spaced 5 m morphisms), an observation interpreted as evidence for apart. Sampling plots were spatially arranged in “blocks” of gene-specific selective sweeps. However, positive selection two plots across the meadow, and one of the two plots in acting on a genomic locus in a recombining population can each block received extended spring rainfall [31]. Samples also leave additional locus-specific signals, including higher were collected over a period of 2 months before and fol- linkage disequilibrium (a strong association between lowing autumn rainfall, resulting in 10 samples per plot alleles) and different allele frequencies between populations
Load more

Recommended publications
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Searching for Replication Help in All of the Rec Places
    Colloquium Historical overview: Searching for replication help in all of the rec places Michael M. Cox* Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544 For several decades, research into the mechanisms of genetic The new awareness of links between replication and recom- recombination proceeded without a complete understanding of its bination was highlighted in a major National Academy of cellular function or its place in DNA metabolism. Many lines of Sciences symposium held Nov. 10–12, 2000 at the Beckman research recently have coalesced to reveal a thorough integration Center in Irvine, California. The breadth of the topic is clear of most aspects of DNA metabolism, including recombination. In from the talks presented at the conference and the papers in this bacteria, the primary function of homologous genetic recombina- issue of PNAS (see summary article by Kuzminov, ref. 204). This tion is the repair of stalled or collapsed replication forks. Recom- report is an attempt to outline the historical paths leading to the binational DNA repair of replication forks is a surprisingly common new focus on the role of recombination at stalled replication process, even under normal growth conditions. The new results forks. I am regularly reminded and readily acknowledge that feature multiple pathways for repair and the involvement of many links between replication and recombination extend well beyond enzymatic systems. The long-recognized integration of replication the re-establishment of replication forks. However, nonmuta- and recombination in the DNA metabolism of bacteriophage T4 has genic replication fork repair provides a uniquely compelling moved into the spotlight with its clear mechanistic precedents.
    [Show full text]
  • Chapter 29 DNA As the Genetic Material Recombination Of
    BCH 4054 Chapter 29 Lecture Notes Slide 1 Chapter 29 DNA: Genetic Information, Recombination, and Mutation Slide 2 DNA as the Genetic Material • Griffith Experiment on pneumococcal transformation (Fig 29.1) • Avery, MacLeod and McCarty showed the principle was DNA • Hershey-Chase experiment on bacteriophage infection (Fig 29.3) • DNA and coat protein labeled differently. Slide 3 Recombination of DNA • Mendel recognized how genes could rearrange in different combinations, with some genes being linked and sorting together • Explained by random sorting of chromosomes • Some linkages weren’t complete, with some rearrangement of pieces of chromosomes Chapter 29, Page 1 Slide 4 Recombination in Meiosis • Sister chromatids pair duing meiosis • Chromosome ends can exchange in a process called “crossing over” • Occurs with equal probability along entire chromosome • Frequency of recombination measures distance between genes, and is used for mapping Slide 5 Importance of Recombination • Phenomenon seen in many different situations • Provides a means for nature to “experiment” • Probably important in evolution of new combinations of genes and pieces of genes • Also important in salvaging damaged genes • Lets look at some specific examples Slide 6 Recombination in Bacteria • Lederberg-Tatum experiments on rearrangement of genes between strains of bacteria (Fig 29.4) • Explanation comes from sexual conjugation followed by genetic recombination • F factor is plasmid carrying genes for conjugation (Fig 29.6) Chapter 29, Page 2 Slide 7 Hfr stands for “high frequency of recombination” Recombination in Bacteria, con’t. • F factor integration into bacterial chromosome creates Hfr cells • Integrated F factor plus part of chromosome is transferred. • Creates diploid condition for some genes.
    [Show full text]
  • Commentary Recombinational Crossroads: Eukaryotic Enzymes and the Limits of Bacterial Precedents
    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 11764–11766, October 1997 Commentary Recombinational crossroads: Eukaryotic enzymes and the limits of bacterial precedents Michael M. Cox* Department of Biochemistry, University of Wisconsin, 420 Henry Mall, Madison, WI 53706 Biochemical form is shaped by biological function. Biochem- terparts are substantial. The DNA strand exchange reactions ical investigation of enzymes involved in eukaryotic homolo- promoted by the human Rad51 and Dmc1 are much less robust gous genetic recombination now is progressing rapidly, having than those promoted by RecA protein (1, 17, 18). ATP is only recently been inaugurated with the study of Rad51 hydrolyzed by all of the eukaryotic proteins at rates from 1 to protein, a homolog of the bacterial RecA protein. A significant 2 orders of magnitude slower than RecA protein. If Rad51 and new front is opened with the first report on the in vitro activities Dmc1 are the eukaryotic equivalents to RecA, evolution seems of a second and meiosis-specific RecA homolog, the human to have served up some markedly hobbled proteins for use in Dmc1 protein (1). Results on Rad51 and Dmc1 to date have eukaryotic recombination. yielded a number of surprises in the form of some intriguing Biological paradigms can both aid and hinder a biochemical and perhaps unanticipated differences with respect to the investigation. In bacteria, the functional paradigm that has RecA protein. Pondering biochemical differences must inev- shaped most in vitro investigations involving RecA is centered itably bring one back to a fundamental question: why do cells on conjugational recombination. However, a strong case can recombine DNA? be made that recombination evolved in bacteria not as a means The history of in vitro research into mechanisms of genetic to exchange genetic information between cells, but as a DNA recombination now spans two decades.
    [Show full text]
  • RECOMBINATION in BACTERIA Transfer of Genetic Material In
    RECOMBINATION IN BACTERIA Transfer of Genetic Material in Bacteria The process of transfer of genetic material and recombination is very interesting bascterial recombination is given (PPT. an overview of bacterial recombination).The three main mechanisms by which bacteria acquire new DNA are transformation, conjugation, and transduction. Transformation involves acquisition of DNA from the environment, conjugation involves acquisition of DNA directly from another bacterium, and transduction involves acquisition of bacterial DNA via a bacteriophage intermediate. Transformation Transformation is the process by which bacteria pick up DNA from their environment. The DNA may come from a variety of sources, but most likely it is the remnants of DNA from dead bacterial cells. In order to become successfully transformed, bacteria must be competent. This means that the bacteria are expressing the appropriate enzymes (the 'transformation machinery') required to transport the exogenous DNA into the cell. Therefore, the correct genes must be expressed in order to carry out transformation. Expression of these genes depends on the growth conditions: bacteria most likely to be competent are dividing rapidly, but nutrients in the environment are becoming limited. (For more on the control of gene expression, see the module on bacterial gene regulation. In transformation, a cell surface receptor binds to DNA in the environment. After binding, the DNA is transported across the membrane by the transformation machinery. As this occurs, one strand of the DNA is digested away by an exonuclease, so that the DNA that enters the cell is single stranded. This promotes recombination, as long as the DNA taken up is sufficiently homologous to the host DNA to allow recombination to occur.
    [Show full text]
  • The Role of Junk DNA
    The role of Junk DNA Agoni Valentina [email protected] Abstract Many efforts have been done in order to explain the role of junk DNA, but its function remain to be elucidated. In addition the GC-content variations among species still represent an enigma. Both these two mysteries can have a common explanation: we hypothesize that the role of junk DNA is to preserve the mutations probability that is intrinsically reduced in GC-poorest genomes. ~ ~ Over 98% of the human genome is noncoding DNA [1]. Initially, a large proportion of noncoding DNA had no known biological function and was therefore sometimes referred to as "junk DNA". The term "junk DNA" was formalized in 1972 by Susumu Ohno[2]. However, some noncoding DNA is transcribed into functional non-coding RNA molecules, e.g. transfer RNA, ribosomal RNA, regulatory RNAs, some other sequences include origins of replication, centromeres and telomeres. Over 8% of the human genome is made up of (mostly decayed) endogenous retrovirus sequences, as part of the over 42% fraction that is recognizably derived of retrotransposons, while another 3% can be identified to be the remains of DNA transposons. Much of the remaining half of the genome that is currently without an explained origin is expected to have found its origin in transposable elements that were active so long ago (> 200 million years) that random mutations have rendered them unrecognizable [3]. Genome size variation in at least two kinds of plants is mostly the result of retrotransposon sequences [4][5]. Pseudogenes are dysfunctional relatives of genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell [6].
    [Show full text]
  • Homologous Recombination in Bacteriophages, Less Fidelity for More Exchanges Geoffrey Hutinet
    Homologous recombination in Bacteriophages, less fidelity for more exchanges Geoffrey Hutinet To cite this version: Geoffrey Hutinet. Homologous recombination in Bacteriophages, less fidelity for more exchanges. Bacteriology. Université Paris Sud - Paris XI, 2014. English. NNT : 2014PA112290. tel-01152135 HAL Id: tel-01152135 https://tel.archives-ouvertes.fr/tel-01152135 Submitted on 15 May 2015 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. UNIVERSITÉ PARIS-SUD ÉCOLE DOCTORALE 435 : AGRICULTURE, ALIMENTATION, BIOLOGIE, ENVIRONNEMENT ET SANTÉ Laboratoire : MICALIS THÈSE DE DOCTORAT SUR TRAVAUX SCIENCES AGRONOMIQUES, BIOTECHNOLOGIES AGRO-ALIMENTAIRES par Geoffrey HUTINET Homologous recombination in Bacteriophages : less fidelity for more exchanges Date de soutenance : 31/10/2014 Composition du jury : Directeur de thèse : Marie-Agnès PETIT Directeur de Recherches (INRA) Président du jury : Cécile FAIRHEAD Professeur (Université Paris Sud XI) Rapporteurs : Mart KRUPOVIC Chargé de Recherches (Institut Pasteur) Stéphanie MARSIN Directeur de Recherches (CEA) Examinateurs : François ENAULT Maitre de Conférences (Université Blaise Pascale) Mauro MODESTI Directeur de Recherches (CNRS) 2 To the truth 3 4 Remerciements Ce que m’a appris ce doctorat sur la recherche peut se résumer par le célèbre adage d’Edward A. Murphy Jr., plus connu sous le nom de loi de Murphy, « Anything that can go wrong, will go wrong » (« Tout ce qui peut mal tourner va mal tourner »).
    [Show full text]