Relevant bibliographies by topics / Bacterial genetic transformation

Academic literature on the topic 'Bacterial genetic transformation'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Bacterial genetic transformation"

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HÅVARSTEIN, LEIV SIGVE. "Bacterial Gene Transfer by Natural Genetic Transformation." APMIS 106, S84 (November 1998): 43–46. http://dx.doi.org/10.1111/j.1600-0463.1998.tb05647.x.

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Draghi, Jeremy A., and Paul E. Turner. "DNA secretion and gene-level selection in bacteria." Microbiology 152, no. 9 (September 1, 2006): 2683–88. http://dx.doi.org/10.1099/mic.0.29013-0.

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Natural genetic transformation can facilitate gene transfer in many genera of bacteria and requires the presence of extracellular DNA. Although cell lysis can contribute to this extracellular DNA pool, several studies have suggested that the secretion of DNA from living bacteria may also provide genetic material for transformation. This paper reviews the evidence for specific secretion of DNA from intact bacteria into the extracellular environment and examines this behaviour from a population-genetics perspective. A mathematical model demonstrates that the joint action of DNA secretion and transformation creates a novel type of gene-level natural selection. This model demonstrates that gene-level selection could explain the existence of DNA secretion mechanisms that provide no benefit to individual cells or populations of bacteria. Additionally, the model predicts that any trait affecting DNA secretion will experience selection at the gene level in a transforming population. This analysis confirms that the secretion of DNA from intact bacterial cells is fully explicable with evolutionary theory, and reveals a novel mechanism for bacterial evolution.
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Engelstädter, Jan, and Danesh Moradigaravand. "Adaptation through genetic time travel? Fluctuating selection can drive the evolution of bacterial transformation." Proceedings of the Royal Society B: Biological Sciences 281, no. 1775 (January 22, 2014): 20132609. http://dx.doi.org/10.1098/rspb.2013.2609.

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Natural transformation is a process whereby bacteria actively take up DNA from the surrounding environment and incorporate it into their genome. Natural transformation is widespread in bacteria, but its evolutionary significance is still debated. Here, we hypothesize that transformation may confer a fitness advantage in changing environments through a process we term ‘genetic time travel’: by taking up old genes that were retained in the environment, the bacteria may revert to a past genotypic state that proves advantageous in the present or a future environment. We scrutinize our hypothesis by means of a mathematical model involving two bacterial types (transforming and non-transforming), a single locus under natural selection and a free DNA pool. The two bacterial types were competed in environments with changing selection regimes. We demonstrate that for a wide range of parameter values for the DNA turnover rate, the transformation rate and the frequency of environmental change, the transforming type outcompetes the non-transforming type. We discuss the empirical plausibility of our hypothesis, as well as its relationship to other hypotheses for the evolution of transformation in bacteria and sex more generally, speculating that ‘genetic time travel’ may also be relevant in eukaryotes that undergo horizontal gene transfer.
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Ambur, Ole Herman, Jan Engelstädter, Pål J. Johnsen, Eric L. Miller, and Daniel E. Rozen. "Steady at the wheel: conservative sex and the benefits of bacterial transformation." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1706 (October 19, 2016): 20150528. http://dx.doi.org/10.1098/rstb.2015.0528.

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Many bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes. This article is part of the themed issue ‘Weird sex: the underappreciated diversity of sexual reproduction’.
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Udayabhanu, Jinu, Tiandai Huang, Shichao Xin, Jing Cheng, Yuwei Hua, and Huasun Huang. "Optimization of the Transformation Protocol for Increased Efficiency of Genetic Transformation in Hevea brasiliensis." Plants 11, no. 8 (April 14, 2022): 1067. http://dx.doi.org/10.3390/plants11081067.

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The recurring growth of bacterium in newly developed resistant cells and a minimal level of bacterial infection rate are the main limiting factors of Agrobacterium-mediated transformation experiments in Hevea brasiliensis. The current study aimed to optimize crucial factors of the transformation protocol in order to obtain an efficient transformation experimental model for Hevea using cotyledonary somatic embryos as explants. Transformation conditions such as antibiotic concentration, preculture duration, Agrobacterium concentration, sonication and cocultivation conditions were analyzed using the binary vector pCAMBIA2301. Transient transformation was confirmed by GUS histochemical staining. The best transformation efficiency was observed when the explants were not cultured on a preculture medium that contained acetosyringone at a level of 100 μM. The best results were obtained using a bacterial density of 0.45 at OD 600 nm, 50 s of sonication of explants in a bacterial liquid culture and a total incubation time of 18 min in the same bacterial suspension. Transmission electron microscopical analysis confirmed the impacts of sonication on bacterial infection efficiency. Cocultivation conditions of 22 °C and 84 h of darkness were optimal for the transfer of T-DNA. Agrobacterium was eliminated with 500 mg/L of timentin, and the selection of transformants was performed using 100 mg/L of kanamycin in the selection medium. The presence of transgene was confirmed in the resistant embryos by polymerase chain reaction (PCR). The improved method of genetic transformation established in the present study will be useful for the introduction of foreign genes of interest into the Hevea genome for the breeding of this economically important plant species in the future.
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Beard, C. B., S. L. O'Neill, P. Mason, L. Mandelco, C. R. Woese, R. B. Tesh, F. F. Richards, and S. Aksoy. "Genetic transformation and phylogeny of bacterial symbionts from tsetse." Insect Molecular Biology 1, no. 3 (February 1993): 123–31. http://dx.doi.org/10.1111/j.1365-2583.1993.tb00113.x.

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Majewski, Jacek, Piotr Zawadzki, Paul Pickerill, Frederick M. Cohan, and Christopher G. Dowson. "Barriers to Genetic Exchange between Bacterial Species: Streptococcus pneumoniae Transformation." Journal of Bacteriology 182, no. 4 (February 15, 2000): 1016–23. http://dx.doi.org/10.1128/jb.182.4.1016-1023.2000.

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ABSTRACT Interspecies genetic exchange is an important evolutionary mechanism in bacteria. It allows rapid acquisition of novel functions by transmission of adaptive genes between related species. However, the frequency of homologous recombination between bacterial species decreases sharply with the extent of DNA sequence divergence between the donor and the recipient. In Bacillus andEscherichia, this sexual isolation has been shown to be an exponential function of sequence divergence. Here we demonstrate that sexual isolation in transformation between Streptococcus pneumoniae recipient strains and donor DNA from related strains and species follows the described exponential relationship. We show that the Hex mismatch repair system poses a significant barrier to recombination over the entire range of sequence divergence (0.6 to 27%) investigated. Although mismatch repair becomes partially saturated, it is responsible for 34% of the observed sexual isolation. This is greater than the role of mismatch repair inBacillus but less than that in Escherichia. The remaining non-Hex-mediated barrier to recombination can be provided by a variety of mechanisms. We discuss the possible additional mechanisms of sexual isolation, in view of earlier findings fromBacillus, Escherichia, andStreptococcus.
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Lorenz, M. G., and W. Wackernagel. "Bacterial gene transfer by natural genetic transformation in the environment." Microbiological Reviews 58, no. 3 (1994): 563–602. http://dx.doi.org/10.1128/mmbr.58.3.563-602.1994.

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Lorenz, M. G., and W. Wackernagel. "Bacterial gene transfer by natural genetic transformation in the environment." Microbiological Reviews 58, no. 3 (1994): 563–602. http://dx.doi.org/10.1128/mr.58.3.563-602.1994.

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Johnston, Christopher D., Sean L. Cotton, Susan R. Rittling, Jacqueline R. Starr, Gary G. Borisy, Floyd E. Dewhirst, and Katherine P. Lemon. "Systematic evasion of the restriction-modification barrier in bacteria." Proceedings of the National Academy of Sciences 116, no. 23 (May 16, 2019): 11454–59. http://dx.doi.org/10.1073/pnas.1820256116.

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Bacteria that are recalcitrant to genetic manipulation using modern in vitro techniques are termed genetically intractable. Genetic intractability is a fundamental barrier to progress that hinders basic, synthetic, and translational microbiology research and development beyond a few model organisms. The most common underlying causes of genetic intractability are restriction-modification (RM) systems, ubiquitous defense mechanisms against xenogeneic DNA that hinder the use of genetic approaches in the vast majority of bacteria and exhibit strain-level variation. Here, we describe a systematic approach to overcome RM systems. Our approach was inspired by a simple hypothesis: if a synthetic piece of DNA lacks the highly specific target recognition motifs for a host’s RM systems, then it is invisible to these systems and will not be degraded during artificial transformation. Accordingly, in this process, we determine the genome and methylome of an individual bacterial strain and use this information to define the bacterium’s RM target motifs. We then synonymously eliminate RM targets from the nucleotide sequence of a genetic tool in silico, synthesize an RM-silent “SyngenicDNA” tool, and propagate the tool as minicircle plasmids, termed SyMPL (SyngenicDNA Minicircle Plasmid) tools, before transformation. In a proof-of-principle of our approach, we demonstrate a profound improvement (five orders of magnitude) in the transformation of a clinically relevant USA300 strain of Staphylococcus aureus. This stealth-by-engineering SyngenicDNA approach is effective, flexible, and we expect in future applications could enable microbial genetics free of the restraints of restriction-modification barriers.
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Dissertations / Theses on the topic "Bacterial genetic transformation"

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Cook, Marisa Anne. "Replicons derived from endogenously isolated plasmids used to classify plasmids occurring in marine sediment bacteria." Thesis, Georgia Institute of Technology, 2001. http://hdl.handle.net/1853/25736.

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Hazen, Tracy Heather. "Genetic elements and molecular mechanisms driving the evolution of the pathogenic marine bacterium Vibrio parahaemolyticus." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/29611.

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Thesis (Ph.D)--Biology, Georgia Institute of Technology, 2010.
Committee Chair: Patricia Sobecky; Committee Member: Eric Stabb; Committee Member: Jim Spain; Committee Member: Roger Wartell; Committee Member: Thomas DiChristina. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Fullner, Karla Jean. "The pilus assembly and T-DNA transfer machinery of Agrobacterium tumefaciens /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/11497.

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Caro, Quintero Alejandro. "The role of horizontal gene transfer in bacterial evolution." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/48979.

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Horizontal gene transfer (HGT) is probably the most important mechanism for functional novelty and adaption in bacteria. However, a robust understanding of the rates of HGT for most bacterial species and the influence of the ecological settings on the rates remain elusive. Four whole-genome comparative studies of free-living bacteria will be described that integrated physiological and ecological data with novel detection bioinformatic pipelines to elucidate the magnitude of HGT at three distinct levels of genetic relatedness: i) the species level, where overlapping ecological niche among co-occurring bacteria in the water column of the Baltic Sea has caused HGT to have been so rampant that it has served as the force of species cohesion; ii) the genus level, where HGT appeared to predominantly mobilize a limited number of genes with ecological/selective advantage (e.g., antibiotic resistance genes) among distinct pathogenic Campylobacter species and hence, did not lead to species convergence; and iii) the phylum level, where HGT was found to be, in general, less frequent than the genus level but, over evolutionary time, has assembled a large part of the metabolic functions of natural microbial communities, especially within organic matter rich, anaerobic habitats. In conclusion, this work advances the methods to link ecological relationships with HGT and suggests that HGT among very divergent organisms may have been more frequent than previously thought and led to successful adaptation.
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Antonova, Elena S. "The regulatory network controlling natural competence for DNA uptake in Vibrio cholerae." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47626.

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The bacterial pathogen Vibrio cholerae is responsible for ongoing cholera outbreaks in Haiti and elsewhere. Association of V. cholerae with the human host is responsible for fatal disease, but the bacteria also reside as natural inhabitants of aquatic environments, commonly attaching as biofilms to chitinous surfaces of copepods and crabs. Prior studies in V. cholerae demonstrated that competence for genetic transformation, a mechanism of horizontal gene transfer (HGT), requires the TfoX regulator protein that is triggered by chitin, and the HapR transcription factor that is made in response to quorum sensing (QS) signals produced by V. cholerae and Vibrios. To define regulatory components connecting extracellular signals to natural competence, I first demonstrated that QS molecules produced by Vibrios within multi-species chitinous biofilms are required for DNA uptake by V. cholerae, confirming the critical role of QS signals in HGT. Second, I identified by transposon-mutagenesis a new positive regulator of competence, CytR (cytidine repressor), only studied prior in E. coli as a regulator of nucleoside scavenging. Specific mutations in V. cholerae CytR impaired expression of competence genes and halted DNA uptake; and the addition of exogenous cytidine had similar affects as predicted in E. coli. V. cholerae and other competent Vibrios encode TfoX, HapR, and CytR, although none of these regulators directly controls genes coding for the DNA uptake apparatus. Thus, these results have uncovered a regulatory network, likely used by many Vibrios, that contains additional factors linking several extracellular chemical molecules (cytidine, chitin, and QS signals) to DNA uptake. My study has begun to define a molecular mechanism by which both environment and genetics contribute to genome evolution for this important marine pathogen.
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Parsons, Stephen H. "Comparing orchid transformation using agrobacterium tumefaciens and particle bombardment." Virtual Press, 1995. http://liblink.bsu.edu/uhtbin/catkey/941350.

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The Wheeler Orchid Collection is home to some of the most endangered species of orchids in the world. This fantastic reservoir of endangered species has been enhanced and broadened by its function as a plant rescue station for the U.S. customs service. Unfortunately, this responsibility increases the risk of bringing orchids, which harbor contageous diseases, into the greenhouse where sap transmitted diseases such as the Tobacco Mosaic Virus (TMV), can run rampant. Although manipulation of orchid characteristics is typically done by classical plant breeding techniques, genetic engineering is emerging as a useful technique for the introduction of desirable traits into the orchid genome. Through the use of genetic engineering techniques it may be possible to mitigate the symptoms associated with this destructive virus. Virus resistance may be achieved through the expression of either the sense or antisense viral coat protein gene in orchid tissues if an efficient means of orchid transformation is developed. In this research two transformation protocols were examined for their ability to efficiently transform orchid tissue. The first transformation protocol explored utilized the native ability of Aq bacterium tumefaciens to incorporate DNA into host plants to achieve transformation. The second mechanism explored was particle bombardment transformation.Many strains of A. tumefaciens were employed using direct exposure of Cattleya_ orchid protocorm and callus tissue. Particle bombardment using DNA coated 0.5 um diameter tungsten particles and high pressure helium tank acceleration was employed. The particle bombardment procedure employed the pG35barB plasmid which confers herbicide resistance to the herbicide basta when integrated and expressed in plant tissues.GUS fluorescence assays and PCR analysis indicate that T-DNA is present in orchid tissues, while Southern blot analysis was unable to display that integration had occurred. Particle bombardment yielded herbicide resistant orchid tissues which have yet to be analyzed by Southern blot analysis to confirm integration due to limited tissue quantities.
Department of Biology
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Hutchinson, Chad M. "Agrobacterium tumefaciens mediated transformation of orchid tissue with the sense and antisense coat protein genes from the odontoglossum ringspot virus." Virtual Press, 1992. http://liblink.bsu.edu/uhtbin/catkey/834608.

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This research was an attempt to use a dicot transformation vector to transform a monocot. The initial purpose of this thesis was to transform orchids with the sense and antisense coat protein genes from the Odontoglossum ringspot virus (ORSV) in an effort to mitigate viral symptoms in transgenic plants using the transformation vector, Agrobacterium tumefaciens. However, it soon became apparent that much time would be needed to develop a transformation protocol. The transformation vectors used included the Agrobacterium tumefaciens disarmed strain LBA4404 with the binary plasmid pB1121, the disarmed strain At699 with the binary plasmid pCNL65, and the wild-type strain Chry5. The marker gene on the binary plasmids of both disarmed strains was p-glucuronidase (GUS).Several transformation protocols were used in an effort to determine if this transformation system would work on orchids. Transformation was not achieved even though a number of experimental conditions were varied. These included using two different types of orchid tissue, callus and protocorms; using two different species of orchids, Cattleya Chocolate Drop x Cattleytonia Kieth Roth and Cymbidium maudidum; varying the time the plant tissue was exposed to the bacteria from 1 hour to 96 hours; performing experiments with and without the wound signal molecule acetosyringone; and exposing the tissue to the virulent strains of A. tumefaciens mentioned previously.This research also developed GUS assay conditions necessary to decrease the number of false positives due to bacterial contamination. These conditions included chloramphenicol in the GUS assay buffer.
Department of Biology
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Jani, Mehul. "Genomic Island Discovery through Enrichment of Statistical Modeling with Biological Information." Thesis, University of North Texas, 2018. https://digital.library.unt.edu/ark:/67531/metadc1248417/.

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Horizontal gene transfer enables acquisition and dissemination of novel traits including antibiotic resistance and virulence among bacteria. Frequently such traits are gained through the acquisition of clusters of functionally related genes, often referred to as genomic islands (GIs). Quantifying horizontal flow of GIs and assessing their contributions to the emergence and evolution of novel metabolic traits in bacterial organisms are central to understanding the evolution of bacteria in general and the evolution of pathogenicity and antibiotic resistance in particular, a focus of this dissertation study. Methods for GI detection have also evolved with advances in sequencing and bioinformatics, however, comprehensive assessment of these methods has been lacking. This motivated us to assess the performance of current methods for identifying islands on broad datasets of well-characterized bacterial genomes and synthetic genomes, and leverage this information to develop a novel approach that circumvents the limitations of the current state-of-the-art in GI detection. The main findings from our assessment studies were 1) the methods have complementary strengths, 2) a gene-clustering method utilizing codon usage bias as the discriminant criterion, namely, JS-CB, is most efficient in localizing genomic islands, specifically the well-studied SCCmec resistance island in methicillin resistant Staphylococcus aureus (MRSA) genomes, and 3) in general, the bottom up, gene by gene analysis methods, are inherently limited in their ability to decipher large structures such as GIs as single entities within bacterial genomes. We adapted a top-down approach based on recursive segmentation and agglomerative clustering and developed a GI prediction tool, GEMINI, which combined compositional features with segment context information to localize GIs in the Liverpool epidemic strain of Pseudomonas aeruginosa. Application of GEMINI to the genome of P. aeruginosa LESB58 demonstrated its ability to delineate experimentally verified GIs in the LESB58 genome. GEMINI identified several novel islands including pathogenicity islands and revealed the mosaic structure of several LESB58 harbored GIs. A new GI identification approach, CAFE, with broad applicability was developed. CAFE incorporates biological information encoded in a genome within the statistical framework of segmentation and clustering to more robustly localize GIs in the genome. CAFE identifies genomic islands lacking markers by virtue of their association with genomic islands with markers originating from the same source. This is made possible by performing marker enrichment and phyletic pattern analyses within the integrated framework of recursive segmentation and clustering. CAFE compared favorably with frequently used methods for genomic island detection on synthetic test datasets and on a test-set of known islands from 15 well-characterized bacterial species. These tools can be readily adapted for cataloging GIs in just sequenced, yet uncharacterized genomes.
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Saavedra, De Bast Manuel. "Systèmes Ta de la famille ccd, de simples gènes égoïstes?" Doctoral thesis, Universite Libre de Bruxelles, 2009. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210045.

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Les systèmes toxine-antitoxine (TA) sont très répandus au sein des génomes bactériens. Ces opérons bicistroniques de petite taille ont été découverts sur des plasmides à bas nombre de copies. Dans ce contexte génétique, les systèmes TA confèrent un avantage sélectif à leurs molécules-hôtes en tuant les bactéries-filles qui ne les ont pas héritées par le mécanisme de tuerie post-ségrégationnelle (PSK, post-segregational killing). Ces systèmes génétiques sont également appelés modules d’addiction étant donné qu’ils rendent la descendance des bactéries qui les contiennent dépendantes de leur présence. Alors que leur rôle dans les molécules d’ADN épisomiques est relativement bien établi, le sens biologique de la présence d’homologues à ces systèmes épisomiques au sein des chromosomes bactériens est sujet à d’intenses débats. L’idée que les systèmes TA chromosomiques confèrent un avantage sélectif a été mise en évidence dans plusieurs modèles. Selon ces modèles, les systèmes TA permettent aux bactéries de mieux faire face à des conditions environnementales stressantes.

Entre-temps, la compréhension de l’évolution des génomes bactériens a connu des avancées significatives. L’impressionnante capacité d’adaptation des bactéries est aujourd’hui majoritairement attribuée au transfert horizontal de gènes (THG) provoqué par les éléments génétiques mobiles (phages, plasmides, transposons…). Dans le débat du rôle des systèmes TA chromosomiques, très peu d’attention a été accordée aux relations phylogénétiques et interactions entre systèmes plasmidiques et chromosomiques co-existant au sein d’un même hôte ainsi qu’à l’impact du THG sur leur évolution. Notre travail de thèse vise à mieux comprendre la biologie des systèmes TA en tenant compte de ces paramètres. Nous nous sommes intéressés à des systèmes homologues au système plasmidique ccdF. Nous avons étudié expérimentalement les 4 systèmes ccd (ccd1, ccd2, ccd3 et ccd4) qui co-habitent au sein du chromosome d’Erwinia chrysanthemi 3937 (une bactérie phytopathogène), leurs interactions intragénomiques et les interactions de ces systèmes avec le système plasmidique ccdF. Ce cadre expérimental a mené à la construction du modèle d’anti-addiction. Ce modèle propose que certains systèmes chromosomiques puissent conférer un avantage sélectif à leurs hôtes bactériens en interférant avec le PSK médié par leurs homologues plasmidiques. Cet avantage sélectif pourrait permettre la fixation de systèmes TA latéralement acquis au sein des populations bactériennes. Nous avons également recherché de nouveaux systèmes ccd au sein des génomes bactériens afin d’avoir un aperçu de leur distribution, des contextes génétiques dans lesquels ils existent et de l’implication du THG dans leur dispersion. Les réflexions qui ont accompagné notre recherche nous ont mené à proposer une synthèse sur le rôle des systèmes TA (plasmidiques et chromosomiques). Celle-ci se nourrit des avancées qui ont été effectuées, ces dernières années, dans la compréhension de l’évolution des génomes bactériens, de la théorie hiérarchique de la sélection naturelle et des processus non-adaptatifs et contingents qui pourraient expliquer la présence et la propagation des systèmes TA au sein des génomes bactériens sans que ceux-ci en soient les agents causaux.


Doctorat en sciences, Spécialisation biologie moléculaire
info:eu-repo/semantics/nonPublished

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Kapadia, Jaimin Maheshbhai. "DNA transfer in the soil bacterium Rhodococcus." Digital Commons @ East Tennessee State University, 2020. https://dc.etsu.edu/honors/565.

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Gene transfer plays an important role in bacterial evolution. Especially in an under explored species like Rhodococcus, a type of bacteria found in the soil. Rhodococcus has several applications in the pharmaceutical industry and in the production of antibiotics. Rhodococcus possess several unique sets of properties which makes it beneficial to have a reliable method of producing mutants of Rhodococcus. The goal of the experiment was to find an efficient way of forming Rhodococcus colonies with kanamycin resistant genes. The project began from an unexpected observation from an earlier experiment with Rhodococcus strain MTM3W5.2. where I attempted to transform this strain with a transposon via electro-transformation. The colonies that grew/ appeared transformants were screened to confirm the presence of kanamycin gene, however there was no amplified DNA seen on the PCR gel (i.e. absence of the kanamycin gene). The electro-transformant colonies were selected on LB plates containing different higher concentrations of kanamycin. Then the appeared transformants were again screened via disk diffusion assay and were classified into 3 different kanamycin resistant phenotypes. Majority of the “C” phenotypic colonies (i.e., high level resistance to kanamycin) appear to contain the kanamycin gene, but these colonies were less in numbers. This led us to try another method of gene transfer which is conjugation. Conjugation was carried on a double selection antibiotic plate containing both chloramphenicol (30 µg) and kanamycin (100 µg). The transconjugate colonies that appeared on the double selection plates were also screened by PCR, but none of the colonies had amplified DNA suggesting absence of the kanamycin gene. The colonies seen on the double selection plate were possibly due to spontaneous mutation or some type of unknown phenotypic variation. However, in the future, double selection plates with higher concentrations of antibiotics can possibly give us transconjugants with kanamycin genes.
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Books on the topic "Bacterial genetic transformation"

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Babu, M. Madan. Bacterial gene regulation and transcriptional networks. Norfolk, UK: Caister Academic Press, 2013.

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Salyers, Abigail A. Antibiotic resistance transfer in the mammalian intestinal tract. New York: Springer, 1995.

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J, Gauthier Michel, ed. Gene transfers and environment: Proceedings of the Third European Meeting on Bacterial Genetics and Ecology (BAGECO-3), 20-22 November 1991, Villefranche-sur-Mer, France. Berlin: Springer-Verlag, 1992.

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Grinius, L. Energy transduction and gene transfer in chemotrophic bacteria: Macromolecules on the move. Chur, Switzerland: Harwood Academic Publishers, 1987.

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E, Vance Dennis, and Vance Jean E, eds. Biochemistry of lipids, lipoproteins, and membranes. Amsterdam: Elsevier, 1991.

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Bacterial transformation [videorecording]. L:ogan: Taped Techologies, 1990.

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Xu, Jimin. Development of genetic exchange systems for Xenorhabdus. 1989, 1989.

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1959-, Mullany Peter, ed. The dynamic bacterial genome. Cambridge: Cambridge University Press, 2005.

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Mullany, Peter. The Dynamic Bacterial Genome (Advances in Molecular and Cellular Microbiology). Cambridge University Press, 2005.

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Wyckoff, Herbert Allen. Development and use of genetic techniques for study of dairy Leuconostoc bacteria. 1992.

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Book chapters on the topic "Bacterial genetic transformation"

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Birge, Edward A. "Genetic Transformation." In Bacterial and Bacteriophage Genetics, 199–219. New York, NY: Springer New York, 1988. http://dx.doi.org/10.1007/978-1-4757-1995-6_8.

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Birge, Edward A. "Genetic Transformation." In Bacterial and Bacteriophage Genetics, 257–76. New York, NY: Springer New York, 1994. http://dx.doi.org/10.1007/978-1-4757-2328-1_10.

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Birge, Edward A. "Genetic Transformation." In Bacterial and Bacteriophage Genetics, 315–39. New York, NY: Springer New York, 2000. http://dx.doi.org/10.1007/978-1-4757-3258-0_10.

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Wackernagel, W. "Persistence of DNA in the Environment and Its Potential for Bacterial Genetic Transformation." In Transgenic Organisms and Biosafety, 137–46. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-642-61460-6_14.

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Srivastava, Sheela. "Transformation." In Genetics of Bacteria, 91–107. India: Springer India, 2013. http://dx.doi.org/10.1007/978-81-322-1090-0_4.

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Ormerod, J. G. "Natural Genetic Transformation in Chlorobium." In Green Photosynthetic Bacteria, 315–19. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4613-1021-1_37.

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Redfield, Rosemary J. "Three Histories of Competence and Transformation." In The Lure of Bacterial Genetics, 277–89. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555816810.ch28.

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Dower, William J. "Electroporation of Bacteria: A General Approach to Genetic Transformation." In Genetic Engineering, 275–95. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4613-0641-2_14.

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González, J. M., A. W. B. Johnston, M. Vila-Costa, and A. Buchan. "Genetics and Molecular Features of Bacterial Dimethylsulfoniopropionate (DMSP) and Dimethylsulfide (DMS) Transformations." In Handbook of Hydrocarbon and Lipid Microbiology, 1201–11. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-77587-4_83.

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González, J. M., A. W. B. Johnston, M. Vila-Costa, and A. Buchan. "Genetics and Molecular Features of Bacterial Dimethylsulfoniopropionate (DMSP) and Dimethyl Sulfide (DMS) Transformations." In Aerobic Utilization of Hydrocarbons, Oils, and Lipids, 773–84. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-50418-6_26.

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Reports on the topic "Bacterial genetic transformation"

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Ron, Eliora, and Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7695860.bard.

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The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.
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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.

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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.
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Reisch, Bruce, Avichai Perl, Julie Kikkert, Ruth Ben-Arie, and Rachel Gollop. Use of Anti-Fungal Gene Synergisms for Improved Foliar and Fruit Disease Tolerance in Transgenic Grapes. United States Department of Agriculture, August 2002. http://dx.doi.org/10.32747/2002.7575292.bard.

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Original objectives . 1. Test anti-fungal gene products for activity against Uncinula necator, Aspergillus niger, Rhizopus stolonifer and Botrytis cinerea. 2. For Agrobacterium transformation, design appropriate vectors with gene combinations. 3. Use biolistic bombardment and Agrobacterium for transformation of important cultivars. 4. Characterize gene expression in transformants, as well as level of powdery mildew and Botrytis resistance in foliage of transformed plants. Background The production of new grape cultivars by conventional breeding is a complex and time-consuming process. Transferring individual traits via single genes into elite cultivars was proposed as a viable strategy, especially for vegetatively propagated crops such as grapevines. The availability of effective genetic transformation procedures, the existence of genes able to reduce pathogen stress, and improved in vitro culture methods for grapes, were combined to serve the objective of this proposal. Effective deployment of resistance genes would reduce production costs and increase crop quality, and several such genes and combinations were used in this project. Progress The efficacy of two-way combinations of Trichoderma endochitinase (CHIT42), synthetic peptide ESF12 and resveratrol upon the control of growth of Botrytis cinerea and Penicillium digitatum were evaluated in vitro. All pairwise interactions were additive but not synergistic. Per objective 2, suitable vectors with important gene combinations for Agrobacterium transformation were designed. In addition, multiple gene co-transformation by particle bombardment was also tested successfully. In New York, transformation work focused on cultivars Chardonnay and Merlot, while the technology in Israel was extended to 41B, R. 110, Prime, Italia, Gamay, Chardonnay and Velika. Transgenic plant production is summarized in the appendix. Among plants developed in Israel, endochitinase expression was assayed via the MuchT assay using material just 1-5 days after co-cultivation. Plants of cv. Sugraone carrying the gene coding for ESF12, a short anti-fungal lytic peptide under the control of the double 358 promoter, were produced. Leaf extracts of two plants showed inhibition zones that developed within 48 h indicating the inhibitory effect of the leaf extracts on the six species of bacteria. X fastidiosa, the causal organism of Pierce's disease, was very sensitive to leaf extracts from ESF12 transformed plants. Further work is needed to verify the agricultural utility of ESF12 transformants. In New York, some transformants were resistant to powdery mildew and Botrytis fruit rot. Major conclusions, solutions, achievements and implications The following scientific achievements resulted from this cooperative BARD project: 1. Development and improvement of embryogenesis and tissue culture manipulation in grape, while extending these procedures to several agriculturally important cultivars both in Israel and USA. 2. Development and improvement of novel transformation procedures while developing transformation techniques for grape and other recalcitrant species. 3. Production of transgenic grapevines, characterization of transformed vines while studying the expression patterns of a marker gene under the control of different promoter as the 35S CaMV in different part of the plants including flowers and fruits. 4. Expression of anti-fungal genes in grape: establishment of transgenic plants and evaluation of gene expression. Development of techniques to insert multiple genes. 5. Isolation of novel grape specific promoter to control the expression of future antimicrobial genes. It is of great importance to report that significant progress was made in not only the development of transgenic grapevines, but also in the evaluation of their potential for increased resistance to disease as compared with the non engineered cultivar. In several cases, increased disease resistance was observed. More research and development is still needed before a product can be commercialized, yet our project lays a framework for further investigations.
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Schuster, Gadi, and David Stern. Integration of phosphorus and chloroplast mRNA metabolism through regulated ribonucleases. United States Department of Agriculture, August 2008. http://dx.doi.org/10.32747/2008.7695859.bard.

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New potential for engineering chloroplasts to express novel traits has stimulated research into relevant techniques and genetic processes, including plastid transformation and gene regulation. This proposal continued our long time BARD-funded collaboration research into mechanisms that influence chloroplast RNA accumulation, and thus gene expression. Previous work on cpRNA catabolism has elucidated a pathway initiated by endonucleolytic cleavage, followed by polyadenylation and exonucleolytic degradation. A major player in this process is the nucleus-encoded exoribonuclease/polymerasepolynucleotidephoshorylase (PNPase). Biochemical characterization of PNPase has revealed a modular structure that controls its RNA synthesis and degradation activities, which in turn are responsive to the phosphate (P) concentration. However, the in vivo roles and regulation of these opposing activities are poorly understood. The objectives of this project were to define how PNPase is controlled by P and nucleotides, using in vitro assays; To make use of both null and site-directed mutations in the PNPgene to study why PNPase appears to be required for photosynthesis; and to analyze plants defective in P sensing for effects on chloroplast gene expression, to address one aspect of how adaptation is integrated throughout the organism. Our new data show that P deprivation reduces cpRNA decay rates in vivo in a PNPasedependent manner, suggesting that PNPase is part of an organismal P limitation response chain that includes the chloroplast. As an essential component of macromolecules, P availability often limits plant growth, and particularly impacts photosynthesis. Although plants have evolved sophisticated scavenging mechanisms these have yet to be exploited, hence P is the most important fertilizer input for crop plants. cpRNA metabolism was found to be regulated by P concentrations through a global sensing pathway in which PNPase is a central player. In addition several additional discoveries were revealed during the course of this research program. The human mitochondria PNPase was explored and a possible role in maintaining mitochondria homeostasis was outlined. As polyadenylation was found to be a common mechanism that is present in almost all organisms, the few examples of organisms that metabolize RNA with no polyadenylation were analyzed and described. Our experiment shaded new insights into how nutrient stress signals affect yield by influencing photosynthesis and other chloroplast processes, suggesting strategies for improving agriculturally-important plants or plants with novel introduced traits. Our studies illuminated the poorly understood linkage of chloroplast gene expression to environmental influences other than light quality and quantity. Finely, our finding significantly advanced the knowledge about polyadenylation of RNA, the evolution of this process and its function in different organisms including bacteria, archaea, chloroplasts, mitochondria and the eukaryotic cell. These new insights into chloroplast gene regulation will ultimately support plant improvement for agriculture
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