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Academic literature on the topic 'Escherichia coli genome'

Author: Grafiati

Published: 6 September 2023

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Journal articles on the topic "Escherichia coli genome"

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Méric, Guillaume, Matthew D. Hitchings, Ben Pascoe, and Samuel K. Sheppard. "From Escherich to the Escherichia coli genome." Lancet Infectious Diseases 16, no. 6 (June 2016): 634–36. http://dx.doi.org/10.1016/s1473-3099(16)30066-4.

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Mori, Hideo, Hiroshi Mizoguchi, and Tatsuro Fujio. "Escherichia coli minimum genome factory." Biotechnology and Applied Biochemistry 46, no. 3 (March 1, 2007): 157. http://dx.doi.org/10.1042/ba20060107.

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Cui, Tailin, Naoki Moro‐oka, Katsufumi Ohsumi, Kenichi Kodama, Taku Ohshima, Naotake Ogasawara, Hirotada Mori, Barry Wanner, Hironori Niki, and Takashi Horiuchi. "Escherichia coli with a linear genome." EMBO reports 8, no. 2 (January 12, 2007): 181–87. http://dx.doi.org/10.1038/sj.embor.7400880.

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Kolisnychenko, V. "Engineering a Reduced Escherichia coli Genome." Genome Research 12, no. 4 (April 1, 2002): 640–47. http://dx.doi.org/10.1101/gr.217202.

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KOOB, MICHAEL D., ANITA J. SHAW, and DOUGLAS C. CAMERON. "Minimizing the Genome of Escherichia coli." Annals of the New York Academy of Sciences 745, no. 1 (December 17, 2006): 1–3. http://dx.doi.org/10.1111/j.1749-6632.1994.tb44359.x.

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Cochrane, Ryan R., Stephanie L. Brumwell, Arina Shrestha, Daniel J. Giguere, Samir Hamadache, Gregory B. Gloor, David R. Edgell, and Bogumil J. Karas. "Cloning of Thalassiosira pseudonana’s Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli." Biology 9, no. 11 (October 26, 2020): 358. http://dx.doi.org/10.3390/biology9110358.

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Algae are attractive organisms for biotechnology applications such as the production of biofuels, medicines, and other high-value compounds due to their genetic diversity, varied physical characteristics, and metabolic processes. As new species are being domesticated, rapid nuclear and organelle genome engineering methods need to be developed or optimized. To that end, we have previously demonstrated that the mitochondrial genome of microalgae Phaeodactylum tricornutum can be cloned and engineered in Saccharomyces cerevisiae and Escherichia coli. Here, we show that the same approach can be used to clone mitochondrial genomes of another microalga, Thalassiosira pseudonana. We have demonstrated that these genomes can be cloned in S. cerevisiae as easily as those of P. tricornutum, but they are less stable when propagated in E. coli. Specifically, after approximately 60 generations of propagation in E. coli, 17% of cloned T. pseudonana mitochondrial genomes contained deletions compared to 0% of previously cloned P. tricornutum mitochondrial genomes. This genome instability is potentially due to the lower G+C DNA content of T. pseudonana (30%) compared to P. tricornutum (35%). Consequently, the previously established method can be applied to clone T. pseudonana’s mitochondrial genome, however, more frequent analyses of genome integrity will be required following propagation in E. coli prior to use in downstream applications.

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Hayashi, Tetsuya. "Genome plasticity of Escherichia coli; insights from genome analysis." Environmental Mutagen Research 27, no. 2 (2005): 117–18. http://dx.doi.org/10.3123/jems.27.117.

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Kang, Yisheng, Tim Durfee, Jeremy D. Glasner, Yu Qiu, David Frisch, Kelly M. Winterberg, and Frederick R. Blattner. "Systematic Mutagenesis of the Escherichia coli Genome." Journal of Bacteriology 186, no. 15 (August 1, 2004): 4921–30. http://dx.doi.org/10.1128/jb.186.15.4921-4930.2004.

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ABSTRACT A high-throughput method has been developed for the systematic mutagenesis of the Escherichia coli genome. The system is based on in vitro transposition of a modified Tn5 element, the Sce-poson, into linear fragments of each open reading frame. The transposon introduces both positive (kanamycin resistance) and negative (I-SceI recognition site) selectable markers for isolation of mutants and subsequent allele replacement, respectively. Reaction products are then introduced into the genome by homologous recombination via the λRed proteins. The method has yielded insertion alleles for 1976 genes during a first pass through the genome including, unexpectedly, a number of known and putative essential genes. Sce-poson insertions can be easily replaced by markerless mutations by using the I-SceI homing endonuclease to select against retention of the transposon as demonstrated by the substitution of amber and/or in-frame deletions in six different genes. This allows a Sce-poson-containing gene to be specifically targeted for either designed or random modifications, as well as permitting the stepwise engineering of strains with multiple mutations. The promiscuous nature of Tn5 transposition also enables a targeted gene to be dissected by using randomly inserted Sce-posons as shown by a lacZ allelic series. Finally, assessment of the insertion sites by an iterative weighted matrix algorithm reveals that these hyperactive Tn5 complexes generally recognize a highly degenerate asymmetric motif on one end of the target site helping to explain the randomness of Tn5 transposition.

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Kang, Yisheng, Tim Durfee, Jeremy D. Glasner, Yu Qiu, David Frisch, Kelly M. Winterberg, and Frederick R. Blattner. "Systematic Mutagenesis of the Escherichia coli Genome." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8548. http://dx.doi.org/10.1128/jb.186.24.8548.2004.

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Pallen, Mark. "Escherichia Coli: From Genome Sequences to Consequence." Canadian Journal of Infectious Diseases and Medical Microbiology 17, no. 2 (2006): 114–16. http://dx.doi.org/10.1155/2006/345319.

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The present article summarizes a presentation given by Professor Mark Pallen of the School of Medicine at the University of Birmingham (Birmingham, United Kingdom) for the Fourth Stanier Lecture held in Regina, Saskatchewan, on November 9, 2004. Professor Pallen's lecture, entitled 'Escherichia coli: From genome sequences to consequences', provides a summary of the important discoveries of his team of research scientists in the area of genetic sequencing and variations in phenotypic expression.

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Dissertations / Theses on the topic "Escherichia coli genome"

1

Neelakanta, Girish. "Genome variations in commensal and pathogenic E.coli." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974330329.

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Schlegel, Susan. "From protein production to genome evolution in Escherichia coli." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-94993.

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The aim of my Ph.D. studies was to improve production yields of membrane- and secretory proteins in the widely used E. coli protein production strain BL21(DE3). In this strain expression of the gene encoding the protein of interest is driven by the powerful T7 RNA polymerase (T7 RNAP) whose gene is located on the chromosome and under control of the strong, IPTG-inducible lacUV5 promoter. Unfortunately, the production of many membrane and secretory proteins is 'toxic' to BL21(DE3), resulting in poor growth and low production yields. To understand this ‘toxicity’, the BL21(DE3) derived mutant strains C41(DE3) and C43(DE3) were characterized. Somehow, these strains can efficiently produce many ‘toxic’ membrane and secretory proteins. We showed that mutations weakening the lacUV5 promoter are responsible for this. These mutations result in a slower onset of protein production upon the addition of IPTG, which avoids saturating the Sec-translocon capacity. The Sec-translocon is a protein-conducting channel in the cytoplasmic membrane mediating the biogenesis of membrane proteins and translocation of secretory proteins. Next, we constructed a BL21(DE3)-derivative, Lemo21(DE3), in which the activity of T7 RNAP can be precisely controlled by titrating in its natural inhibitor T7 lysozyme using the rhamnose promoter system. In Lemo21(DE3), the expression level of genes encoding membrane and secretory proteins can be set such that the Sec-translocon capacity is not saturated. This is key to optimizing membrane and secretory protein production yields. Finally, reconstructing the evolution of C41(DE3) from BL21(DE3) in real time showed that during its isolation C41(DE3) had acquired mutations critical for surviving the starvation conditions used, and provided insight in how the mutations in the lacUV5 promoter had occurred.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

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Romero, Alvarez David. "Genome wide analyses of the Escherichia coli primary and secondary transcriptomes." Thesis, University of Leeds, 2014. http://etheses.whiterose.ac.uk/6917/.

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Escherichia coli K12 serves as an important model for studying systems that are important to bacteria in their own right as well as those that are conserved in ‘higher' organisms, which are more difficult and costly to study. Like many model organisms, the genome of K12 has been sequenced, producing a catalogue of protein-coding and stable-RNA genes that enabled study using ‘omic’ approaches. This has led to a rapid expansion of our knowledge of patterns of gene expression and their dependency on growth conditions, cell physiology and individual genes. However, the underlying networks of gene regulation are less well understood, but are known to involve the control of steps in RNA processing and degradation as well as transcription and translation. With this in mind, this thesis describes the development of an approach based on RNA sequencing that produces nucleotide-resolution transcriptome maps that distinguish sites that correspond to RNA processing and steps in degradation from those of transcription initiation, while incorporating all classes of RNA. Comparison with results obtained previously validated the approach, which has been applied already to the study of other bacterial species. Within the E. coli map, many new features were identified, such as previously undetected small RNAs and processing at a site associated with the production of specialised ribosomes, which may ensure the translation of leaderless mRNAs, which were also mapped. The approach also showed the benefit of incorporating steps that can differentiate the 5’ status of transcripts in assigning sites of transcription initiation. RNA sequencing was also used to map sites of cleavage by RNase E, an essential endoribonuclease that is central to both the processing and degradation of RNA in bacteria and plant plastids. This aspect of the thesis has advanced from pilot studies to the point where the ‘code’ that determines one form of substrate recognition by RNase E is beginning to emerge. As a result of this success, equivalent data has been collected for other ribonucleases involved in RNA processing and degradation. Continuing analysis of the primary and secondary transcriptomes, consisting of native, unprocessed transcripts and of transcripts that have been modified from their native form via processing and/or degradation respectively, with the tools presented here promises to broaden and deepen our understanding of an important model organism.

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Coss, Dennis. "Insertion of genes and operons into the Escherichia coli genome through targeted recombination." Morgantown, W. Va. : [West Virginia University Libraries], 2005. https://eidr.wvu.edu/etd/documentdata.eTD?documentid=3804.

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Thesis (Ph. D.)--West Virginia University, 2005.
Title from document title page. Document formatted into pages; contains v, 125 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 71-87).

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Mosberg, Joshua Adam Weintrob. "Studying and Improving Lambda Red Recombination for Genome Engineering in Escherichia coli." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10777.

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The phage-derived Lambda Red recombination system utilizes exogenous DNA in order to generate precise insertion, deletion, and point mutations in Escherichia coli and other bacteria. Due to its convenience, it is a frequently-used tool in genetics and molecular biology, as well as in larger-scale genome engineering projects. However, limited recombination frequency constrains the usefulness of Lambda Red for several important applications. In this work, I utilize a mechanism-guided approach in order to improve the power and utility of Lambda Red recombination.

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Schmidt, Dorothea. "Molekulare Analyse des probiotischen Stamms Escherichia coli Nissle 1917." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2009. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1243973355362-88295.

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Der probiotische Stamm E. coli Nissle 1917 ist ein Fäkalisolat, das in der Medizin traditionell zur Behandlung verschiedener gastrointestinaler Erkrankungen eingesetzt wird. Durch erfolgversprechende klinische Studien zur Remissionserhaltung bei Colitis ulcerosa, bei denen EcN als therapeutische Alternative zur Standardmedikation eingesetzt wird, ist das Interesse an den Wirkmechanismen von Probiotika stark gestiegen. EcN gehört derzeit zu den am besten untersuchten Probiotika. Einige Wirkmechanismen konnten dadurch schon aufgeklärt werden. So sind vermutlich Strukturkomponenten und stammspezifische Syntheseleistungen an der Ausprägung des probiotischen Phänotyps von EcN beteiligt. Schlüssige Konzepte, die über Gene, Genprodukte und molekulare Mechanismen den probiotischen Effekt von EcN erklären, fehlen bislang. Im Rahmen dieser Arbeit wird das Genom von EcN analysiert und auf der Basis der Genomsequenz mit anderen E. coli-Stämmen verglichen. Mit Hilfe einer Promotor-Reporter-Fusionsbibliothek (Promotorbank) werden intestinal in vivo regulierte Gene identifiziert und dadurch neue Ansätze zur Untersuchung der probiotischen Eigenschaften von EcN geschaffen. Die Grundlage für die molekulare Analyse von EcN ist die manuelle Nachannotation seines sequenzierten Genoms. Die EcN-Sequenz wird mit 13 weiteren annotierten E. coli-Sequenzen verglichen. Nach dieser Analyse kodiert EcN derzeit 121 stammspezifische Gene. Die Genomstruktur ist mit den enthaltenen genomischen Inseln und Prophagen dem Genom des uropathogenen E. coli CFT073 sehr ähnlich. Mit wenigen Ausnahmen kodiert EcN alle in E. coli CFT073 vorhandenen Virulenz- und Fitnessfaktoren, so dass auf der Nukleotidebene die nahe Verwandschaft dieser beiden Stämme bestätigt werden kann. Zudem kann gezeigt werden, dass EcN in artifiziellen Systemen wie der Zellkultur oder gnotobiotischen Mäusen ein pathogenes Potenzial hat, obgleich die Kolonisierungsfähigkeit pathogener Bakterien durch Inkubation mit EcN herabgesetzt wird. Eine wichtige Rolle bei der Besiedlung des Intestinaltrakts und der Immunstimulation von Darmepithelzellen spielt auch die globale Regulation der Genaktivität bei EcN durch den alternativen Sigma-Faktor RpoS, der im Gegensatz zu rpoS-Deletionsmutanten zu einer gesteigerten mRNA-Expression des Tight-junction Proteins ZO-1 führt. Des Weiteren führte die Untersuchung von EcN-Deletionsmutanten zu der Schlussfolgerung, dass einige genomische Inseln für Eigenschaften, die das probiotische Verhalten erklären können, eine Rolle spielen. Durch den Einsatz einer Promotorbank von EcN in konventionellen und gnotobiotischen Mäusen werden erstmalig Sequenzen von intestinal in vivo aktiven Promotoren identifiziert. Der Aufbau eines Promotor-Reportergen-Assays mit dem Biolumineszenz erzeugenden luxCDABE-Operon ermöglichte die Untersuchung ausgewählter Promotoren in vitro. Mit einem In Vivo Imaging System (IVIS) kann in weiteren Experimenten die Aktivität dieser Promotoren in lebenden Mäusen untersucht werden. Im Rahmen dieser Arbeit wird gezeigt, dass EcN kein vollkommen harmloser probiotischer Stamm ist. Weitere Informationen über EcN sind dehalb wichtig für eine optimierte Anwendung als Therapeutikum. Die molekulare Analyse ist somit eine unbedingt notwendige Grundlage für weiterführende Untersuchungen der Eigenschaften von EcN, die für seinen probiotischen Charakter verantwortlich sind
The probiotic E. coli Nissle 1917 is a fecal isolate which is traditionally used for treatment of various gastrointestinal disorders. In clinical trials where EcN was used as therapeutic alternative for remission maintenance of ulcerative colitis compared to standard medication, promising results led to an increased interest in probiotics. Today, EcN is one of the best studied probiotics. Therefore, several mechanisms of action could be enlightened. Structural components and strain-specific products are responsible for its probiotic effects. But conclusive concepts about genes, gene products and molecular mechanisms that really contribute to the probiotic character of EcN have not been offered so far. In order to create new possibilities to elucidate the probiotic traits of EcN the genome is analysed by taking this as a basis for comparison to other E. coli genomes and identification of intestinal in vivo regulated genes using a promoter-trap-library. The sequenced EcN genome is annotated and compared to 13 other so far annotated E. coli genomes. Concerning these analyses EcN encodes 121 strain-specific genes. The genome structure including the genomic islands and prophages is highly homolog to the uropathogenic E. coli CFT073. EcN encodes most of the virulence and fitness factors that are present in E. coli CFT073. Therefore, the close relationship of these two strains is confirmed at nucleotide level. Furthermore, it is shown that in artificial systems like cell culture assays and gnotobiotic mice EcN reveals a pathogenic potential although EcN is able to decrease colonization efficiency of pathogenic bacteria. The alternative sigma factor RpoS that is responsible for global regulation and activity of several genes seems to play an important role during colonization of EcN in the intestine and its immunostimulatory effects on intestinal epithelial cells. Investigation of EcN-deletion mutants lacking genomic islands and prophages lead to the conclusion that some genomic islands may play a role for specific probiotic traits. This is the first time where a promoter-trap-library was used in conventional and gnotobiotic mice for collection of intestinal in vivo active promoters. Constructing and establishing a promoter-reporter gene assay with the bioluminescent luxCDABE operon made the investigation of selected promoters in vitro possible as well as establishing a bioluminescence assay using an In Vivo Imaging System (IVIS) for investigation of promoter activity in living mice. In this research project was shown that EcN is not a completely harmless probiotic. The genome structure and regulatory mechanisms of gene expression are the strain’s molecular traits that lead to probiotic activity and immunostimulatory effects. Therefore, the molecular analyses presented here, together with the complete genome sequence, are a basis for further investigations of mechanisms that are responsible for the probiotic effects of EcN

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Coulange, Frédérique. "Isolement et caracterisation de regions specifiques du genome des escherichia coli pathogenes aviaires (doctorat : microbiologie)." Paris 11, 1999. http://www.theses.fr/1999PA114802.

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PRADEL, NATHALIE. "Escherichia coli producteurs de shiga-toxines : etude epidemiologique, recherche des caracteristiques des souches pathogenes par comparaison moleculaire et hybridation soustractive (doctorat : microbiologie)." Clermont-Ferrand 1, 2001. http://www.theses.fr/2001CLF1PP02.

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Brambilla, Elisa. "Investigation of E. coli genome complexity by means of fluorescent reporters of gene expression." Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066607/document.

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Escherichia coli est capable de survivre dans de nombreux environnements différents. Les informations nécessaires à cette adaptation sont codées dans le chromosome. Cette molécule circulaire est condensé dans une structure compacte protéines-ADN, appelée nucléoïde. Le chromosome n¿est pas uniforme et montre notamment une distribution inégale de sites de fixation de protéines et de séquences riches en AT. Il a été montré que la position des gènes importants pour la cellule est hautement conservée dans les gamma-protéobactéries. Ces différences le long du chromosome et cette conservation de la position suggèrent que la position du gène peut influencer son expression. Pour tester cette hypothèse, on a étudié l'expression d'un gène fluorescent inséré dans différentes positions autour du chromosome. L'expression de ce gène est contrôlé par des promoteurs différemment régulés: un est réprimé par la protéine H-NS, un est non régulé et un est sensible au superenroulement de l'ADN. Nous avons étudié l'expression dynamique de ces promoteurs pendant les différentes phases de croissance dans différentes conditions. Nous avons montré que l'expression du promoteur dépendant de la protéine H-NS est liée à l'emplacement sur le chromosome. En effet, la répression par H-NS est accrue en présence de séquences riches en AT. Nous avons également étudié l'influence d'un gène divergent sur l'expression de gènes rapporteurs en fonction de la position chromosomique. Nous avons montré que cette influence dépend de la localisation du gène. Nous avons donc demontré l'impact de la position chromosomique sur l'expression des gènes tout en donnant une nouvelle perspective sur la complexité du génome
Escherichia coli is able to survive in many different environments. The information necessary for this adaptation is encoded in the chromosome. This circular molecule is condensed in a compact DNA-protein structure, called the nucleoid. The chromosome is not uniform, and shows uneven distributions of nucleoid-associated proteins (NAPs) binding sites, AT-rich sequences and general protein occupancy domains. It has been demonstrated that the position of important genes is highly conserved in ?-Proteobacteria. These differences along the chromosome and the conserved position of important genes suggest that the position of the gene can influence gene expression. To test this hypothesis, I studied the expression of a fluorescent reporter gene inserted in different positions around the chromosome. The expression of the reporter is driven by differently regulated promoters, one repressed by the important NAP H-NS, one non regulated and one subject to supercoiling and stringent control. We studied the dynamical expression of these promoters in different growth conditions, growth phases, upon nutritional upshift and under stress. We showed that the expression of the H-NS dependent promoter depends on the location on the chromosome, because H-NS repression is enhanced in presence of AT-rich sequences. We also studied the influence of a divergent gene on the reporter expression as a function of chromosomal position, and showed that this influence depends on the location of the gene. With our study we have been therefore able to show the impact of chromosomal position on gene expression and to give a new perspective on genome complexity

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Nguyen, Huong LE. "Etude des facteurs régulateurs de la traduction chez Escherichia coli." Thesis, Toulouse, INSA, 2019. http://www.theses.fr/2019ISAT0004.

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L’analyse des régulations de l’expression des gènes chez les bactéries permet de comprendre l’adaptation des bactéries à leur environnement et dans un contexte de biologie de synthèse d’optimiser la production microbienne de molécules d’intérêt. Notre objectif a été d’étudier la traduction au niveau du génome et ses relations avec les autres processus cellulaires par une approche de biologie des systèmes. Le traductome a été mesuré : pour chacun des ARN messagers, son pourcentage de copies en traduction et sa densité en ribosomes. Pour la première fois, une image complète de l’état traductionnel de E. coli en croissance rapide a été obtenue, caractérisée par une majorité de transcrits avec un très fort pourcentage de copies en traduction mais faiblement chargés en ribosomes. Notre modèle statistique a identifié des facteurs liés à la séquence comme déterminants de la traduction et le rôle important d’un paramètre physiologique : la concentration en ARNm. Pour la première fois, cet effet de la transcription sur la traduction a été validé à l’échelle moléculaire sur plusieurs gènes. Nous avons montré qu’une augmentation de la concentration d’un ARNm par induction transcriptionnelle entrainait une augmentation du pourcentage de copies en traduction et de la charge en ribosomes
The analysis of gene expression regulation is necessary to better understand bacterial adaptation to environment and to be able in a context of synthetic biology to optimize the production of molecules of interest. The goal of this thesis was to study translation at the genome-wide level and its relationship to other cellular processes using a systems biology approach. First, translation activity at the -omic scale (called the traductome) was measured : for each messenger RNAs, its percentage of copies in translation and ribosome density. For the first time, a complete picture of the translational state in fast growing E. coli cells was obtained, characterized by a majority of transcripts with a very high percentage of copies in translation but a low ribosome density. Our model identified sequence-related factors as determinants of translation but, more surprisingly, the model predicted the important role of a physiological parameter: the mRNA concentration. Thus, more concentrated mRNA would have higher percentage of copies in translation and higher ribosome density. For the first time, this effect of transcription on translation has been validated at the molecular level on several genes. We showed that an increase in mRNA concentration by transcriptional induction results in increases in percentage of copies in translation and in ribosome load

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Books on the topic "Escherichia coli genome"

1

Vaillancourt, Peter E. E. coli gene expression protocols. Totowa, N.J: Humana, 2011.

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Magnusson, Lisa. Global regulation of gene expression in Escherichia coli: The role of ppGpp, DksA, and the levels of RNA polymerase. Göteborg: Göteborgs universitet, 2007.

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Magnusson, Lisa. Global regulation of gene expression in Escherichia coli: The role of ppGpp, DksA, and the levels of RNA polymerase. Göteborg: Göteborgs universitet, 2007.

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Heterologous gene expression in E. coli: Methods and protocols. New York, NY: Humana Press, 2011.

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K, Patient R., ed. Genetic engineering. Oxford: IRL Press, 1988.

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A, Ceccarelli, and Wallace A. 1963-, eds. Genetic engineering. 2nd ed. Oxford: Bios, 2001.

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G, Williams J. Genetic engineering. Oxford: BIOS Scientific Publishers, 1993.

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Zdziarski, Jaroslaw. The genesis of asymptomatic bacteriuria Escherichia coli strains: Evolution, bacterial genome plasticity and host-pathogen adaptations of asymptomatic bacteriuria Escherichia coli strains. VDM Verlag Dr. Müller, 2011.

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Lin, E. C. C., and A. Simon Lynch. Regulation of Gene Expression in Escherichia Coli. Springer London, Limited, 2012.

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C, Lin E. C., and Lynch A. Simon 1964-, eds. Regulation of gene expression in Escherichia coli. New York: Chapman & Hall, 1996.

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Book chapters on the topic "Escherichia coli genome"

1

Milkman, Roger. "Gene Transfer in Escherichia coli." In Organization of the Prokaryotic Genome, 291–309. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818180.ch16.

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Jensen, Sheila Ingemann, and Alex Toftgaard Nielsen. "Multiplex Genome Editing in Escherichia coli." In Methods in Molecular Biology, 119–29. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7295-1_8.

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Weinstock, George M. "Resources for the Escherichia coli Genome Project." In Bacterial Genomes, 489–97. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-6369-3_38.

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Fehér, Tamás, Ildikó Karcagi, Zsuzsa Győrfy, Kinga Umenhoffer, Bálint Csörgő, and György Pósfai. "Scarless Engineering of the Escherichia coli Genome." In Microbial Gene Essentiality: Protocols and Bioinformatics, 251–59. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-321-9_16.

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Mellmann, Alexander, Martina Bielaszewska, and Helge Karch. "Genotypic Changes in Enterohemorrhagic Escherichia coli During Human Infection." In Genome Plasticity and Infectious Diseases, 16–26. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555817213.ch2.

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Applebee, M. Kenyon, and Bernhard Ø. Palsson. "Genome-Scale Models and the Genetic Basis for E. coli Adaptation." In Systems Biology and Biotechnology of Escherichia coli, 237–56. Dordrecht: Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-1-4020-9394-4_12.

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Sung, Bong Hyun, Jun Hyoung Lee, and Sun Chang Kim. "Escherichia coli Genome Engineering and Minimization forthe Construction of a Bioengine." In Systems Biology and Biotechnology of Escherichia coli, 19–40. Dordrecht: Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-1-4020-9394-4_2.

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Feist, Adam M., Ines Thiele, and Bernhard Ø. Palsson. "Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network." In Systems Biology and Biotechnology of Escherichia coli, 149–76. Dordrecht: Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-1-4020-9394-4_9.

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Labedan, Bernard, and Monica Riley. "Genetic Inventory: Escherichia coli as a Window on Ancestral Proteins." In Organization of the Prokaryotic Genome, 311–29. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818180.ch17.

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Nouwens, Amanda S., Femia G. Hopwood, Mathew Traini, Keith L. Williams, and Bradley J. Walsh. "Proteome Approach to the Identification of Cellular Escherichia coli Proteins." In Organization of the Prokaryotic Genome, 331–46. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818180.ch18.

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Conference papers on the topic "Escherichia coli genome"

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Huang, Yi. "Codon Effect on the Entire Genome Based upon Genome-Wide Recoded Escherichia coli." In 2021 IEEE 9th International Conference on Bioinformatics and Computational Biology (ICBCB). IEEE, 2021. http://dx.doi.org/10.1109/icbcb52223.2021.9459235.

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Kurmi, Annushree, Debashis Das, Piyali Sen, Suvendra Kumar Ray, and Siddhartha Sankar Satapathy. "Gene Essentiality Mediated Base Substitution in Escherichia coli genome: Machine Learning Analysis." In 2022 International Interdisciplinary Conference on Mathematics, Engineering and Science (MESIICON). IEEE, 2022. http://dx.doi.org/10.1109/mesiicon55227.2022.10093501.

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Meizhen Ji, Jun Lu, Ying Zhang, Changjiang Ding, Dandan Qin, and Haiyan Bai. "Operon prediction based on quadratic discriminant analysis in Escherichia coli genome." In 2010 2nd International Conference on Information Science and Engineering (ICISE). IEEE, 2010. http://dx.doi.org/10.1109/icise.2010.5689023.

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Jia, Mengwen, and Yong Zhan. "Relationship of ORF length and mRNA degradation in Escherichia coli genome." In NUMERICAL ANALYSIS AND APPLIED MATHEMATICS ICNAAM 2012: International Conference of Numerical Analysis and Applied Mathematics. AIP, 2012. http://dx.doi.org/10.1063/1.4756461.

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Vilkhovoy, M., N. Horvath, and J. D. Varner. "Toward genome scale modeling of Escherichia coli cell-free protein synthesis." In IET/SynbiCITE Engineering Biology Conference. Institution of Engineering and Technology, 2016. http://dx.doi.org/10.1049/cp.2016.1253.

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"Impact of terahertz irradiation on the antimicrobial resistance of Escherichia coli JM 103." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-316.

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Teramoto, Jun, Kayoko Yamada, Naoki Kobayashi, Ayako Kori, Shige H. Yoshimura, Kunio Takeyasu, and Akira Ishihama. "Anaerobiosis-induced novel nucleoid protein of Escherichia coli: Architectural role in genome DNA compaction." In 2009 International Symposium on Micro-NanoMechatronics and Human Science (MHS). IEEE, 2009. http://dx.doi.org/10.1109/mhs.2009.5351819.

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"On the question of activity of oxidative branch of pentose phosphate shunt in pgl mutant of Escherichia coli." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-311.

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"The minimal medium irradiated with terahertz radiation induces proteins of homeostasis of transition metal ions and represses proteins of amino acid metabolism when Escherichia coli cells are cultivated on it." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-313.

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Sahlan, Muhamad, Ihsan Wiratama, Heri Hermansyah, Anondho Wijarnako, Mohamad Teguh Gumelar, and Masafumi Yohda. "Apoptin gene optimization in Escherichia coli." In SECOND INTERNATIONAL CONFERENCE OF MATHEMATICS (SICME2019). Author(s), 2019. http://dx.doi.org/10.1063/1.5096733.

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Reports on the topic "Escherichia coli genome"

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Shpigel, Nahum Y., Ynte Schukken, and Ilan Rosenshine. Identification of genes involved in virulence of Escherichia coli mastitis by signature tagged mutagenesis. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699853.bard.

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Mastitis, an inflammatory response of the mammary tissue to invading pathogenic bacteria, is the largest health problem in the dairy industry and is responsible for multibillion dollar economic losses. E. coli are a leading cause of acute mastitis in dairy animals worldwide and certainly in Israel and North America. The species E. coli comprises a highly heterogeneous group of pathogens, some of which are commensal residents of the gut, infecting the mammary gland after contamination of the teat skin from the environment. As compared to other gut microflora, mammary pathogenic E. coli (MPEC) may have undergone evolutionary adaptations that improve their fitness for colonization of the unique and varied environmental niches found within the mammary gland. These niches include competing microbes already present or accompanying the new colonizer, soluble and cellular antimicrobials in milk, and the innate immune response elicited by mammary cells and recruited immune cells. However, to date, no specific virulence factors have been identified in E. coli isolates associated with mastitis. The original overall research objective of this application was to develop a genome-wide, transposon-tagged mutant collection of MPEC strain P4 and to use this technology to identify E. coli genes that are specifically involved in mammary virulence and pathogenicity. In the course of the project we decided to take an alternative genome-wide approach and to use whole genomes bioinformatics analysis. Using genome sequencing and analysis of six MPEC strains, our studies have shown that type VI secretion system (T6SS) gene clusters were present in all these strains. Furthermore, using unbiased screening of MPEC strains for reduced colonization, fitness and virulence in the murine mastitis model, we have identified in MPEC P4-NR a new pathogenicity island (PAI-1) encoding the core components of T6SS and its hallmark effectors Hcp, VgrG and Rhs. Next, we have shown that specific deletions of T6SS genes reduced colonization, fitness and virulence in lactating mouse mammary glands. Our long-term goal is to understand the molecular mechanisms of host-pathogen interactions in the mammary gland and to relate these mechanisms to disease processes and pathogenesis. We have been able to achieve our research objectives to identify E. coli genes that are specifically involved in mammary virulence and pathogenicity. The project elucidated a new basic concept in host pathogen interaction of MPEC, which for the best of our knowledge was never described or investigated before. This research will help us to shed new light on principles behind the infection strategy of MPEC. The new targets now enable prevalence and epidemiology studies of T6SS in field strains of MPEC which might unveil new geographic, management and ecological risk factors. These will contribute to development of new approaches to treat and prevent mastitis by MPEC and perhaps other mammary pathogens. The use of antibiotics in farm animals and specifically to treat mastitis is gradually precluded and thus new treatment and prevention strategies are needed. Effective mastitis vaccines are currently not available, structural components and effectors of T6SS might be new targets for the development of novel vaccines and therapeutics.

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Willis, C., F. Jorgensen, S. A. Cawthraw, H. Aird, S. Lai, M. Chattaway, I. Lock, E. Quill, and G. Raykova. A survey of Salmonella, Escherichia coli (E. coli) and antimicrobial resistance in frozen, part-cooked, breaded or battered poultry products on retail sale in the United Kingdom. Food Standards Agency, May 2022. http://dx.doi.org/10.46756/sci.fsa.xvu389.

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Frozen, breaded, ready-to-cook chicken products have been implicated in outbreaks of salmonellosis. Some of these outbreaks can be large. For example, one outbreak of Salmonella Enteritidis involved 193 people in nine countries between 2018 and 2020, of which 122 cases were in the UK. These ready-to-cook products have a browned, cooked external appearance, which may be perceived as ready-to-eat, leading to mishandling or undercooking by consumers. Continuing concerns about these products led FSA to initiate a short-term (four month), cross-sectional surveillance study undertaken in 2021 to determine the prevalence of Salmonella spp., Escherichia coli and antimicrobial resistance (AMR) in frozen, breaded or battered chicken products on retail sale in the UK. This study sought to obtain data on AMR levels in Salmonella and E. coli in these products, in line with a number of other FSA instigated studies of the incidence and nature of AMR in the UK food chain, for example, the systematic review (2016). Between the beginning of April and the end of July 2021, 310 samples of frozen, breaded or battered chicken products containing either raw or partly cooked chicken, were collected using representative sampling of retailers in England, Wales, Scotland and Northern Ireland based on market share data. Samples included domestically produced and imported chicken products and were tested for E. coli (including extended-spectrum beta-lactamase (ESBL)-producing, colistin-resistant and carbapenem-resistant E. coli) and Salmonella spp. One isolate of each bacterial type from each contaminated sample was randomly selected for additional AMR testing to determine the minimum inhibitory concentration (MIC) for a range of antimicrobials. More detailed analysis based on Whole Genome Sequencing (WGS) data was used to further characterise Salmonella spp. isolates and allow the identification of potential links with human isolates. Salmonella spp. were detected in 5 (1.6%) of the 310 samples and identified as Salmonella Infantis (in three samples) and S. Java (in two samples). One of the S. Infantis isolates fell into the same genetic cluster as S. Infantis isolates from three recent human cases of infection; the second fell into another cluster containing two recent cases of infection. Countries of origin recorded on the packaging of the five Salmonella contaminated samples were Hungary (n=1), Ireland (n=2) and the UK (n=2). One S. Infantis isolate was multi-drug resistant (i.e. resistant to three different classes of antimicrobials), while the other Salmonella isolates were each resistant to at least one of the classes of antimicrobials tested. E. coli was detected in 113 samples (36.4%), with counts ranging from <3 to >1100 MPN (Most Probable Number)/g. Almost half of the E. coli isolates (44.5%) were susceptible to all antimicrobials tested. Multi-drug resistance was detected in 20.0% of E. coli isolates. E. coli isolates demonstrating the ESBL (but not AmpC) phenotype were detected in 15 of the 310 samples (4.8%) and the AmpC phenotype alone was detected in two of the 310 samples (0.6%) of chicken samples. Polymerase Chain Reaction (PCR) testing showed that five of the 15 (33.3%) ESBL-producing E. coli carried blaCTX-M genes (CTX-M-1, CTX-M-55 or CTX-M-15), which confer resistance to third generation cephalosporin antimicrobials. One E. coli isolate demonstrated resistance to colistin and was found to possess the mcr-1 gene. The five Salmonella-positive samples recovered from this study, and 20 similar Salmonella-positive samples from a previous UKHSA (2020/2021) study (which had been stored frozen), were subjected to the cooking procedures described on the sample product packaging for fan assisted ovens. No Salmonella were detected in any of these 25 samples after cooking. The current survey provides evidence of the presence of Salmonella in frozen, breaded and battered chicken products in the UK food chain, although at a considerably lower incidence than reported in an earlier (2020/2021) study carried out by PHE/UKHSA as part of an outbreak investigation where Salmonella prevalence was found to be 8.8%. The current survey also provides data on the prevalence of specified AMR bacteria found in the tested chicken products on retail sale in the UK. It will contribute to monitoring trends in AMR prevalence over time within the UK, support comparisons with data from other countries, and provide a baseline against which to monitor the impact of future interventions. While AMR activity was observed in some of the E. coli and Salmonella spp. examined in this study, the risk of acquiring AMR bacteria from consumption of these processed chicken products is low if the products are cooked thoroughly and handled hygienically.

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Balfanz, Emma, Erin Sandford, Michael G. Kaiser, and Susan J. Lamont. Differential Immunological Gene Expression after Escherichia coli Infection in Chickens. Ames (Iowa): Iowa State University, January 2011. http://dx.doi.org/10.31274/ans_air-180814-668.

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Monson, Melissa S., Michael G. Kaiser, and Susan J. Lamont. Gene Expression Responses to Infection with Avian Pathogenic Escherichia coli in Chicken Spleen. Ames (Iowa): Iowa State University, January 2018. http://dx.doi.org/10.31274/ans_air-180814-329.

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Sandford, Erin, Megan Orr, Xianyao Li, Huaijun Zhou, timothy J. Johnson, Subhashinie Kariyawasam, Lisa K. Nolan, Peng Liu, and Susan J. Lamont. Gene Expression Differences in White Blood Cells after Escherichia coli Infection in Chickens. Ames (Iowa): Iowa State University, January 2012. http://dx.doi.org/10.31274/ans_air-180814-665.

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Gutnick, David, and David L. Coplin. Role of Exopolysaccharides in the Survival and Pathogenesis of the Fire Blight Bacterium, Erwinia amylovora. United States Department of Agriculture, September 1994. http://dx.doi.org/10.32747/1994.7568788.bard.

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Fireblight, a disease of apples and pears, is caused by Erwinia amylovora. Mutants of E. amylovora that do not produce the extreacellular polysaccharide (EPS), amylovoran, are avirulent. A similar EPS, stewartan, is produced by E. stewartii, which caused Stewart's wilt of corn, and which has also been implicated in the virulence of this strain. Both stewartan and amylovoran are type 1 capsular polysaccharides, typified by the colanic acid slime produced by Escherichia coli. Extracellular polysaccharide slime and capsules are important for the virulence of bacterial pathogens of plants and animals and to enhance their survival and dissemination outside of the host. The goals of this project were to examine the importance of polysaccharide structure on the pathogenicity and survival properties of three pathogenic bacteria: Erwinia amylovora, Erwinia stewartii and Escherichia coli. The project was a collaboration between the laboratories of Dr. Gutnick (PI, E. coli genetics and biochemistry), Dr. Coplin (co-PI, E. stewartii genetics) and Dr. Geider (unfunded collaborator, E. amylovora genetics and EPS analysis). Structural analysis of the EPSs, sequence analysis of the biosynthetic gene clusters and site-directed mutagenesis of individual cps and ams genes revealed that the three gene clusters shared common features for polysaccharide polymerization, translocation, and precursor synthesis as well as in the modes of transcriptional regulation. Early EPS production resulted in decreased virulence, indicating that EPS, although required for pathogenicity, is anot always advantageous and pathogens must regulate its production carefully.

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Wackett, Lawrence, Raphi Mandelbaum, and Michael Sadowsky. Bacterial Mineralization of Atrazine as a Model for Herbicide Biodegradation: Molecular and Applied Aspects. United States Department of Agriculture, January 1999. http://dx.doi.org/10.32747/1999.7695835.bard.

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Atrazine is a broadly used herbicide in agriculture and it was used here as a model to study the biodegradation of herbicides. The bacterium Pseudomonas sp. ADP metabolizes atrazine to carbon dioxide and ammonia and chloride. The genes encoding atrazine catabolism to cyanuric acid were cloned and expressed in Escherichia coli. The genes were designated atzA, atzB and atzC. Each gene was sequenced. The enzyme activities were characterized. AtzA is atrazine chlorohydrolase which takes atrazine to hydroxyatrizine. AtzB is hydroxyatrazine N-ethylaminohydrolase which produces N-isopropylammelide and N-ethylamine. AtzC is N-isopropylammelide N-isopropylaminohydrolase which produces cyanuric acid and N-isopropylamine. Each product was isolated and characterized to confirm their identity by chromatography and mass spectrometry. Sequence analysis indicated that each of the hydrolytic enzymes AtzA, AtzB and AtzC share identity which the aminohydrolase protein superfamily. Atrazine chlorohydrolase was purified to homogeneity. It was shown to have a kcat of 11 s-1 and a KM of 150 uM. It was shown to require a metal ion, either Fe(II), Mn(II) or Co(II), for activity. The atzA, atzB and atzC genes were shown to reside on a broad-host range plasmid in Pseudomonas sp. ADP. Six other recently isolated atrazine-degrading bacteria obtained from Europe and the United States contained homologs to the atz genes identified in Pseudomonas sp. ADP. The identity of the sequences were very high, being greater than 98% in all pairwise comparisons. This indicates that many atrazine-degrading bacteria worldwide metabolize atrazine via a pathway that proceeds through hydroxyatrazine, a metabolite which is non-phytotoxic and non-toxic to mammals. Enzymes were immobilized and used for degradation of atrazine in aqueous phases. The in-depth understanding of the genomics and biochemistry of the atrazine mineralization pathway enabled us to study factors affecting the prevalence of atrazine degradation in various agricultural soils under conservative and new agricultural practices. Moreover, Pseudomonas sp. ADP and/or its enzymes were added to atrazine-contaminated soils, aquifers and industrial wastewater to increase the rate and extent of atrazine biodegradation above that of untreated environments. Our studies enhance the ability to control the fate of regularly introduced pesticides in agriculture, or to reduce the environmental impact of unintentional releases.

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Cahaner, Avigdor, Susan J. Lamont, E. Dan Heller, and Jossi Hillel. Molecular Genetic Dissection of Complex Immunocompetence Traits in Broilers. United States Department of Agriculture, August 2003. http://dx.doi.org/10.32747/2003.7586461.bard.

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Objectives: (1) Evaluate Immunocompetence-OTL-containing Chromosomal Regions (ICRs), marked by microsatellites or candidate genes, for magnitude of direct effect and for contribution to relationships among multiple immunocompetence, disease-resistance, and growth traits, in order to estimate epistatic and pleiotropic effects and to predict the potential breeding applications of such markers. (2) Evaluate the interaction of the ICRs with genetic backgrounds from multiple sources and of multiple levels of genetic variation, in order to predict the general applicability of molecular genetic markers across widely varied populations. Background: Diseases cause substantial economic losses to animal producers. Emerging pathogens, vaccine failures and intense management systems increase the impact of diseases on animal production. Moreover, zoonotic pathogens are a threat to human food safety when microbiological contamination of animal products occurs. Consumers are increasingly concerned about drug residues and antibiotic- resistant pathogens derived from animal products. The project used contemporary scientific technologies to investigate the genetics of chicken resistance to infectious disease. Genetic enhancement of the innate resistance of chicken populations provides a sustainable and ecologically sound approach to reduce microbial loads in agricultural populations. In turn, animals will be produced more efficiently with less need for drug treatment and will pose less of a potential food-safety hazard. Major achievements, conclusions and implications:. The PI and co-PIs had developed a refined research plan, aiming at the original but more focused objectives, that could be well-accomplished with the reduced awarded support. The successful conduct of that research over the past four years has yielded substantial new information about the genes and genetic markers that are associated with response to two important poultry pathogens, Salmonella enteritidis (SE) and Escherichia coli (EC), about variation of immunocompetence genes in poultry, about relationships of traits of immune response and production, and about interaction of genes with environment and with other genes and genetic background. The current BARD work has generated a base of knowledge and expertise regarding the genetic variation underlying the traits of immunocompetence and disease resistance. In addition, unique genetic resource populations of chickens have been established in the course of the current project, and they are essential for continued projects. The US laboratory has made considerable progress in studies of the genetics of resistance to SE. Microsatellite-marked chromosomal regions and several specific genes were linked to SE vaccine response or bacterial burden and the important phenomenon of gene interaction was identified in this system. In total, these studies demonstrate the role of genetics in SE response, the utility of the existing resource population, and the expertise of the research group in conducting such experiments. The Israeli laboratories had showed that the lines developed by selection for high or low level of antibody (Ab) response to EC differ similarly in Ab response to several other viral and bacterial pathogens, indicating the existence of a genetic control of general capacity of Ab response in young broilers. It was also found that the 10w-Ab line has developed, possibly via compensatory "natural" selection, higher cellular immune response. At the DNA levels, markers supposedly linked to immune response were identified, as well as SNP in the MHC, a candidate gene responsible for genetic differences in immunocompetence of chickens.

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