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Journal articles on the topic 'Escherichia coli genome'

Author: Grafiati

Published: 6 September 2023

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1

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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2

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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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11

Xie, Ting, Liang-Yu Fu, Qing-Yong Yang, Heng Xiong, Hongrui Xu, Bin-Guang Ma, and Hong-Yu Zhang. "Spatial features for Escherichia coli genome organization." BMC Genomics 16, no. 1 (2015): 37. http://dx.doi.org/10.1186/s12864-015-1258-1.

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12

Mellmann, Alexander, Martina Bielaszewska, and Helge Karch. "Intrahost Genome Alterations in Enterohemorrhagic Escherichia coli." Gastroenterology 136, no. 6 (May 2009): 1925–38. http://dx.doi.org/10.1053/j.gastro.2008.12.072.

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13

Posfai, G. "Emergent Properties of Reduced-Genome Escherichia coli." Science 312, no. 5776 (May 19, 2006): 1044–46. http://dx.doi.org/10.1126/science.1126439.

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14

Tsai, Lu, and Zhirong Sun. "Dynamic flexibility in the Escherichia coli genome." FEBS Letters 507, no. 2 (October 15, 2001): 225–30. http://dx.doi.org/10.1016/s0014-5793(01)02978-7.

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15

Butcher, James. "Geneticists sequence Escherichia coli O157:H7 genome." Lancet 357, no. 9252 (January 2001): 286. http://dx.doi.org/10.1016/s0140-6736(05)71728-1.

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16

Song, J. Y., R. H. Yoo, S. Y. Jang, W. K. Seong, S. Y. Kim, H. Jeong, S. G. Kang, et al. "Genome Sequence of Enterohemorrhagic Escherichia coli NCCP15658." Journal of Bacteriology 194, no. 14 (June 27, 2012): 3749–50. http://dx.doi.org/10.1128/jb.00653-12.

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17

Jeong, Jaehwan, Namjin Cho, Daehee Jung, and Duhee Bang. "Genome-scale genetic engineering in Escherichia coli." Biotechnology Advances 31, no. 6 (November 2013): 804–10. http://dx.doi.org/10.1016/j.biotechadv.2013.04.003.

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18

Dobrindt, Ulrich, Franziska Agerer, Kai Michaelis, Andreas Janka, Carmen Buchrieser, Martin Samuelson, Catharina Svanborg, Gerhard Gottschalk, Helge Karch, and Jörg Hacker. "Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays." Journal of Bacteriology 185, no. 6 (March 15, 2003): 1831–40. http://dx.doi.org/10.1128/jb.185.6.1831-1840.2003.

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ABSTRACT Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was determined using a DNA “pathoarray” developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.

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19

Mori, Hirotada, Masakazu Kataoka, and Xi Yang. "Past, Present, and Future of Genome Modification in Escherichia coli." Microorganisms 10, no. 9 (September 14, 2022): 1835. http://dx.doi.org/10.3390/microorganisms10091835.

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Escherichia coli K-12 is one of the most well-studied species of bacteria. This species, however, is much more difficult to modify by homologous recombination (HR) than other model microorganisms. Research on HR in E. coli has led to a better understanding of the molecular mechanisms of HR, resulting in technical improvements and rapid progress in genome research, and allowing whole-genome mutagenesis and large-scale genome modifications. Developments using λ Red (exo, bet, and gam) and CRISPR-Cas have made E. coli as amenable to genome modification as other model microorganisms, such as Saccharomyces cerevisiae and Bacillus subtilis. This review describes the history of recombination research in E. coli, as well as improvements in techniques for genome modification by HR. This review also describes the results of large-scale genome modification of E. coli using these technologies, including DNA synthesis and assembly. In addition, this article reviews recent advances in genome modification, considers future directions, and describes problems associated with the creation of cells by design.

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20

Chayot, Romain, Benjamin Montagne, Didier Mazel, and Miria Ricchetti. "An end-joining repair mechanism in Escherichia coli." Proceedings of the National Academy of Sciences 107, no. 5 (January 19, 2010): 2141–46. http://dx.doi.org/10.1073/pnas.0906355107.

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Bridging broken DNA ends via nonhomologous end-joining (NHEJ) contributes to the evolution and stability of eukaryote genomes. Although some bacteria possess a simplified NHEJ mechanism, the human commensal Escherichia coli is thought to rely exclusively on homology-directed mechanisms to repair DNA double-strand breaks (DSBs). We show here that laboratory and pathogenic E. coli strains possess a distinct end-joining activity that repairs DSBs and generates genome rearrangements. This mechanism, named alternative end-joining (A-EJ), does not rely on the key NHEJ proteins Ku and Ligase-D which are absent in E. coli. Differently from classical NHEJ, A-EJ is characterized by extensive end-resection largely due to RecBCD, by overwhelming usage of microhomology and extremely rare DNA synthesis. We also show that A-EJ is dependent on the essential Ligase-A and independent on Ligase-B. Importantly, mutagenic repair requires a functional Ligase-A. Although generally mutagenic, accurate A-EJ also occurs and is frequent in some pathogenic bacteria. Furthermore, we show the acquisition of an antibiotic-resistance gene via A-EJ, refuting the notion that bacteria gain exogenous sequences only by recombination-dependent mechanisms. This finding demonstrates that E. coli can integrate unrelated, nonhomologous exogenous sequences by end-joining and it provides an alternative strategy for horizontal gene transfer in the bacterial genome. Thus, A-EJ contributes to bacterial genome evolution and adaptation to environmental challenges. Interestingly, the key features of A-EJ also appear in A-NHEJ, an alternative end-joining mechanism implicated in chromosomal translocations associated with human malignancies, and we propose that this mutagenic repair might have originated in bacteria.

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21

Henry, Christopher S., Matthew D. Jankowski, Linda J. Broadbelt, and Vassily Hatzimanikatis. "Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism." Biophysical Journal 90, no. 4 (February 2006): 1453–61. http://dx.doi.org/10.1529/biophysj.105.071720.

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22

Esnault, Emilie, Michèle Valens, Olivier Espéli, and Frédéric Boccard. "Chromosome Structuring Limits Genome Plasticity in Escherichia coli." PLoS Genetics 3, no. 12 (December 14, 2007): e226. http://dx.doi.org/10.1371/journal.pgen.0030226.

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23

Perna, Nicole T., Guy Plunkett, Valerie Burland, Bob Mau, Jeremy D. Glasner, Debra J. Rose, George F. Mayhew, et al. "Genome sequence of enterohaemorrhagic Escherichia coli O157:H7." Nature 409, no. 6819 (January 2001): 529–33. http://dx.doi.org/10.1038/35054089.

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24

Banno, Satomi, Keiji Nishida, Takayuki Arazoe, Hitoshi Mitsunobu, and Akihiko Kondo. "Deaminase-mediated multiplex genome editing in Escherichia coli." Nature Microbiology 3, no. 4 (February 5, 2018): 423–29. http://dx.doi.org/10.1038/s41564-017-0102-6.

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25

Ussery, David, Thomas Schou Larsen, K. Trevor Wilkes, Carsten Friis, Peder Worning, Anders Krogh, and Søren Brunak. "Genome organisation and chromatin structure in Escherichia coli." Biochimie 83, no. 2 (February 2001): 201–12. http://dx.doi.org/10.1016/s0300-9084(00)01225-6.

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26

Smalley, Darren J., Marvin Whiteley, and Tyrrell Conway. "In search of the minimal Escherichia coli genome." Trends in Microbiology 11, no. 1 (January 2003): 6–8. http://dx.doi.org/10.1016/s0966-842x(02)00008-2.

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27

Bielaszewska, Martina, Ulrich Dobrindt, Julia Gärtner, Inka Gallitz, Jörg Hacker, Helge Karch, Daniel Müller, et al. "Aspects of genome plasticity in pathogenic Escherichia coli." International Journal of Medical Microbiology 297, no. 7-8 (November 2007): 625–39. http://dx.doi.org/10.1016/j.ijmm.2007.03.001.

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28

Li, T., F. Pu, R. Yang, X. Fang, J. Wang, Y. Guo, D. Chang, et al. "Draft Genome Sequence of Escherichia coli LCT-EC106." Journal of Bacteriology 194, no. 16 (July 27, 2012): 4443–44. http://dx.doi.org/10.1128/jb.00853-12.

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29

Boycheva, S., G. Chkodrov, and I. Ivanov. "Codon pairs in the genome of Escherichia coli." Bioinformatics 19, no. 8 (May 22, 2003): 987–98. http://dx.doi.org/10.1093/bioinformatics/btg082.

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30

Madyagol, Mahesh, Hend Al-Alami, Zdeno Levarski, Hana Drahovská, Ján Turňa, and Stanislav Stuchlík. "Gene replacement techniques for Escherichia coli genome modification." Folia Microbiologica 56, no. 3 (May 2011): 253–63. http://dx.doi.org/10.1007/s12223-011-0035-z.

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31

Kurokawa, Masaomi, and Bei-Wen Ying. "Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli." Microorganisms 8, no. 1 (December 18, 2019): 3. http://dx.doi.org/10.3390/microorganisms8010003.

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Genome reduction, as a top-down approach to obtain the minimal genetic information essential for a living organism, has been conducted with bacterial cells for decades. The most popular and well-studied cell models for genome reduction are Escherichia coli strains. As the previous literature intensively introduced the genetic construction and application of the genome-reduced Escherichia coli strains, the present review focuses the design principles and compares the reduced genome collections from the specific viewpoint of growth, which represents a fundamental property of living cells and is an important feature for their biotechnological application. For the extended simplification of the genomic sequences, the approach of experimental evolution and concern for medium optimization are newly proposed. The combination of the current techniques of genomic construction and the newly proposed methodologies could allow us to acquire growing Escherichia coli cells carrying the extensively reduced genome and to address the question of what the minimal genome essential for life is.

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32

Hochhauser, Dina, Adi Millman, and Rotem Sorek. "The defense island repertoire of the Escherichia coli pan-genome." PLOS Genetics 19, no. 4 (April 6, 2023): e1010694. http://dx.doi.org/10.1371/journal.pgen.1010694.

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It has become clear in recent years that anti-phage defense systems cluster non-randomly within bacterial genomes in so-called “defense islands”. Despite serving as a valuable tool for the discovery of novel defense systems, the nature and distribution of defense islands themselves remain poorly understood. In this study, we comprehensively mapped the defense system repertoire of >1,300 strains of Escherichia coli, the most widely studied organism for phage-bacteria interactions. We found that defense systems are usually carried on mobile genetic elements including prophages, integrative conjugative elements and transposons, which preferentially integrate at several dozens of dedicated hotspots in the E. coli genome. Each mobile genetic element type has a preferred integration position but can carry a diverse variety of defensive cargo. On average, an E. coli genome has 4.7 hotspots occupied by defense system-containing mobile elements, with some strains possessing up to eight defensively occupied hotspots. Defense systems frequently co-localize with other systems on the same mobile genetic element, in agreement with the observed defense island phenomenon. Our data show that the overwhelming majority of the E. coli pan-immune system is carried on mobile genetic elements, explaining why the immune repertoire varies substantially between different strains of the same species.

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33

Kim, Yong Chan, Heun Choi, Young Ah Kim, Yoon Soo Park, Young Hee Seo, Hyukmin Lee, and Kyungwon Lee. "Risk factors and microbiological features of recurrent Escherichia coli bloodstream infections." PLOS ONE 18, no. 1 (January 10, 2023): e0280196. http://dx.doi.org/10.1371/journal.pone.0280196.

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Understanding the risk factors and microbiological features in recurrent Escherichia coli BSI is helpful for clinicians. Data of patients with E. coil BSI from 2017 to 2018 were collected. Antimicrobial resistance rates of E. coli were determined. We also identified the ST131 and ESBL genotype to evaluate the molecular epidemiology of E. coli. Whole genome sequencing was conducted on the available ESBL-producing E. coli samples. Of 808 patients with E. coli BSI, 57 (6.31%) experienced recurrence; 29 developed at 4–30 days after initial BSI (early onset recurrence) and 28 at 31–270 days after initial BSI (late onset recurrence). One hundred forty-nine patients with single episode, whose samples were available for determining the molecular epidemiology, were selected for comparison. Vascular catheterization (adjusted odds ratio [aOR], 4.588; 95% confidence interval [CI], 1.049–20.068), ESBL phenotype (aOR, 2.037; 95% CI, 1.037–3.999) and SOFA score ≥9 (aOR, 3.210; 95% CI, 1.359–7.581) were independent risk factors for recurrence. The proportion of ST131 and ESBL genotype was highest in early onset recurrent BSI (41.4% and 41.4%, respectively), from which E. coil had the highest resistance rates to most antimicrobial agents. Whole genome sequencing on 27 of ESBL-producing E. coli (11 from single episode, 11 from early onset recurrence, and 5 from late onset recurrence) demonstrated that various virulence factors, resistant genes, and plasmid types existed in isolates from all types of BSI. Risk factors contributing to the recurrence and microbiological features of E. coli causing recurrent BSI may be helpful for management planning in the clinical setting.

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34

Snipen, Lars-Gustav, and David W. Ussery. "A domain sequence approach to pangenomics: applications to Escherichia coli." F1000Research 1 (October 1, 2012): 19. http://dx.doi.org/10.12688/f1000research.1-19.v1.

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The study of microbial pangenomes relies on the computation of gene families, i.e. the clustering of coding sequences into groups of essentially similar genes. There is no standard approach to obtain such gene families. Ideally, the gene family computations should be robust against errors in the annotation of genes in various genomes. In an attempt to achieve this robustness, we propose to cluster sequences by their domain sequence, i.e. the ordered sequence of domains in their protein sequence. In a study of 347 genomes from Escherichia coli we find on average around 4500 proteins having hits in Pfam-A in every genome, clustering into around 2500 distinct domain sequence families in each genome. Across all genomes we find a total of 5724 such families. A binomial mixture model approach indicates this is around 95% of all domain sequences we would expect to see in E. coli in the future. A Heaps law analysis indicates the population of domain sequences is larger, but this analysis is also very sensitive to smaller changes in the computation procedure. The resolution between strains is good despite the coarse grouping obtained by domain sequence families. Clustering sequences by their ordered domain content give us domain sequence families, who are robust to errors in the gene prediction step. The computational load of the procedure scales linearly with the number of genomes, which is needed for the future explosion in the number of re-sequenced strains. The use of domain sequence families for a functional classification of strains clearly has some potential to be explored.

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35

Snipen, Lars-Gustav, and David W. Ussery. "A domain sequence approach to pangenomics: applications to Escherichia coli." F1000Research 1 (May 29, 2013): 19. http://dx.doi.org/10.12688/f1000research.1-19.v2.

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The study of microbial pangenomes relies on the computation of gene families, i.e. the clustering of coding sequences into groups of essentially similar genes. There is no standard approach to obtain such gene families. Ideally, the gene family computations should be robust against errors in the annotation of genes in various genomes. In an attempt to achieve this robustness, we propose to cluster sequences by their domain sequence, i.e. the ordered sequence of domains in their protein sequence. In a study of 347 genomes from Escherichia coli we find on average around 4500 proteins having hits in Pfam-A in every genome, clustering into around 2500 distinct domain sequence families in each genome. Across all genomes we find a total of 5724 such families. A binomial mixture model approach indicates this is around 95% of all domain sequences we would expect to see in E. coli in the future. A Heaps law analysis indicates the population of domain sequences is larger, but this analysis is also very sensitive to smaller changes in the computation procedure. The resolution between strains is good despite the coarse grouping obtained by domain sequence families. Clustering sequences by their ordered domain content give us domain sequence families, who are robust to errors in the gene prediction step. The computational load of the procedure scales linearly with the number of genomes, which is needed for the future explosion in the number of re-sequenced strains. The use of domain sequence families for a functional classification of strains clearly has some potential to be explored.

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36

Romeo, Lucia, Antonia Esposito, Alberto Bernacchi, Daniele Colazzo, Alberto Vassallo, Marco Zaccaroni, Renato Fani, and Sara Del Duca. "Application of Cloning-Free Genome Engineering to Escherichia coli." Microorganisms 11, no. 1 (January 15, 2023): 215. http://dx.doi.org/10.3390/microorganisms11010215.

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The propagation of foreign DNA in Escherichia coli is central to molecular biology. Recent advances have dramatically expanded the ability to engineer (bacterial) cells; however, most of these techniques remain time-consuming. The aim of the present work was to explore the possibility to use the cloning-free genome editing (CFGE) approach, proposed by Döhlemann and coworkers (2016), for E. coli genetics, and to deepen the knowledge about the homologous recombination mechanism. The E. coli auxotrophic mutant strains FB182 (hisF892) and FB181 (hisI903) were transformed with the circularized wild-type E. coli (i) hisF gene and hisF gene fragments of decreasing length, and (ii) hisIE gene, respectively. His+ clones were selected based on their ability to grow in the absence of histidine, and their hisF/hisIE gene sequences were characterized. CFGE method allowed the recombination of wild-type his genes (or fragments of them) within the mutated chromosomal copy, with a different recombination frequency based on the fragment length, and the generation of clones with a variable number of in tandem his genes copies. Data obtained pave the way to further evolutionary studies concerning the homologous recombination mechanism and the fate of in tandem duplicated genes.

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37

Rasko, David A., M. J. Rosovitz, Garry S. A. Myers, Emmanuel F. Mongodin, W. Florian Fricke, Pawel Gajer, Jonathan Crabtree, et al. "The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates." Journal of Bacteriology 190, no. 20 (August 1, 2008): 6881–93. http://dx.doi.org/10.1128/jb.00619-08.

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ABSTRACT Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.

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38

García, Mauro D., María J. Ruiz, Luis M. Medina, Roberto Vidal, Nora L. Padola, and Analía I. Etcheverria. "Molecular and Genetic Characterization of Colicinogenic Escherichia coli Strains Active against Shiga Toxin-Producing Escherichia coli O157:H7." Foods 12, no. 14 (July 11, 2023): 2676. http://dx.doi.org/10.3390/foods12142676.

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The objective of this work was to molecularly and genotypically characterize and test the inhibitory activity of six colicinogenic Escherichia coli strains (ColEc) and their partially purified colicins against STEC O157:H7 isolated from clinical human cases. Inhibition tests demonstrated the activity of these strains and their colicins against STEC O157:H7. By PCR it was possible to detect colicins Ia, E7, and B and microcins M, H47, C7, and J25. By genome sequencing of two selected ColEc strains, it was possible to identify additional colicins such as E1 and Ib. No genes coding for stx1 and stx2 were detected after analyzing the genome sequence. The inhibitory activity of ColEc against STEC O157:H7 used as an indicator showed that colicins are potent growth inhibitors of E. coli O157:H7, being a potential alternative to reduce the presence of pathogens of public health relevance.

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Chen, Jingchao, Yi Li, Kun Zhang, and Hailei Wang. "Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5α." Genome Announcements 6, no. 10 (March 8, 2018). http://dx.doi.org/10.1128/genomea.00097-18.

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ABSTRACT The genomes of many strains of Escherichia coli have been sequenced, as this organism is a classic model bacterium. Here, we report the genome sequence of Escherichia coli DH5α, which is resistant to a T4 bacteriophage (CCTCC AB 2015375), while its other homologous E. coli strains, such as E. coli BL21, DH10B, and MG1655, are not resistant to phage invasions. Thus, understanding of the genome of the DH5α strain, along with comparative analysis of its genome sequence along with other sequences of E. coli strains, may help to reveal the bacteriophage resistance mechanism of E. coli .

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Khetrapal, Varnica, Kurosh S. Mehershahi, and Swaine L. Chen. "Complete Genome Sequence of the Original Escherichia coli Isolate, Strain NCTC86." Genome Announcements 5, no. 16 (April 20, 2017). http://dx.doi.org/10.1128/genomea.00243-17.

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ABSTRACT Escherichia coli is the most well-studied bacterium and a common colonizer of the lower mammalian gastrointestinal tract. We report here the complete genome sequence of the original Escherichia coli isolate, strain NCTC86, which was described by Theodor Escherich, for whom the genus is named.

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Abram, Kaleb, Zulema Udaondo, Carissa Bleker, Visanu Wanchai, Trudy M. Wassenaar, Michael S. Robeson, and David W. Ussery. "Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups." Communications Biology 4, no. 1 (January 26, 2021). http://dx.doi.org/10.1038/s42003-020-01626-5.

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AbstractIn this study, more than one hundred thousand Escherichia coli and Shigella genomes were examined and classified. This is, to our knowledge, the largest E. coli genome dataset analyzed to date. A Mash-based analysis of a cleaned set of 10,667 E. coli genomes from GenBank revealed 14 distinct phylogroups. A representative genome or medoid identified for each phylogroup was used as a proxy to classify 95,525 unassembled genomes from the Sequence Read Archive (SRA). We find that most of the sequenced E. coli genomes belong to four phylogroups (A, C, B1 and E2(O157)). Authenticity of the 14 phylogroups is supported by several different lines of evidence: phylogroup-specific core genes, a phylogenetic tree constructed with 2613 single copy core genes, and differences in the rates of gene gain/loss/duplication. The methodology used in this work is able to reproduce known phylogroups, as well as to identify previously uncharacterized phylogroups in E. coli species.

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"Large-scale genome editing in Escherichia coli." Nature Methods 8, no. 9 (August 30, 2011): 709. http://dx.doi.org/10.1038/nmeth.1689.

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Soltys, Katarina, Silvia Vavrova, Jaroslav Budis, Lenka Palkova, Gabriel Minarik, and Jozef Grones. "Draft Genome Sequence of Escherichia coli KL53." Genome Announcements 6, no. 13 (March 29, 2018). http://dx.doi.org/10.1128/genomea.00220-18.

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ABSTRACT Here, we report the draft genome sequence of a clinical isolate of the uropathogenic strain Escherichia coli KL53. A total of 5,083,632 bp was de novo assembled into 170 contigs containing 89 RNAs and 5,034 protein-coding genes. Remarkable is the presence of the tellurite resistance ( ter ) operon on a plasmid.

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Brown, Steven D., and Suckjoon Jun. "Complete Genome Sequence of Escherichia coli NCM3722." Genome Announcements 3, no. 4 (August 6, 2015). http://dx.doi.org/10.1128/genomea.00879-15.

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Grenier, F., D. Matteau, V. Baby, and S. Rodrigue. "Complete Genome Sequence of Escherichia coli BW25113." Genome Announcements 2, no. 5 (October 16, 2014). http://dx.doi.org/10.1128/genomea.01038-14.

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Gonzalez-Alba, José Maria, Fernando Baquero, Rafael Cantón, and Juan Carlos Galán. "Stratified reconstruction of ancestral Escherichia coli diversification." BMC Genomics 20, no. 1 (December 2019). http://dx.doi.org/10.1186/s12864-019-6346-1.

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Abstract Background Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still unresolved. A combined strategy based on stratified phylogeny and ancient molecular polymorphisms is proposed to infer detailed evolutionary reconstructions by using a large number of whole genomes. This strategy, based on the highest number of genomes available in public databases, was evaluated for improving knowledge of the ancient diversification of E. coli. This staggered evolutionary scenario was also used to investigate whether the diversification of the ancient E. coli lineages could be associated with particular lifestyles and adaptive strategies. Results Phylogenetic reconstructions, exploiting 6220 available genomes in Genbank, established the E. coli core genome in 1023 genes, representing about 20% of the complete genome. The combined strategy using stratified phylogeny plus molecular polymorphisms inferred three ancient lineages (D, EB1A and FGB2). Lineage D was the closest to E. coli root. A staggered diversification could also be proposed in EB1A and FGB2 lineages and the phylogroups into these lineages. Several molecular markers suggest that each lineage had different adaptive trajectories. The analysis of gained and lost genes in the main lineages showed that functions of carbohydrates utilization (uptake of and metabolism) were gained principally in EB1A lineage, whereas loss of environmental-adaptive functions in FGB2 lineage were observed, but this lineage showed higher accumulated mutations and ancient recombination events. The population structure of E. coli was re-evaluated including up to 7561 new sequenced genomes, showing a more complex population structure of E. coli, as a new phylogroup, phylogroup I, was proposed. Conclusions A staggered reconstruction of E. coli phylogeny is proposed, indicating evolution from three ancestral lineages to reach all main known phylogroups. New phylogroups were confirmed, suggesting an increasingly complex population structure of E. coli. However these new phylogroups represent < 1% of the global E. coli population. A few key evolutionary forces have driven the diversification of the two main E. coli lineages, metabolic flexibility in one of them and colonization-virulence in the other.

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Yesil, Mustafa, En Huang, Xu Yang, and Ahmed E. Yousef. "Complete Genome Sequence of Escherichia Phage OSYSP." Genome Announcements 5, no. 42 (October 19, 2017). http://dx.doi.org/10.1128/genomea.00880-17.

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ABSTRACT Bacteriophage OSYSP is a new anti-Escherichia coli O157:H7 phage isolated from municipal wastewater in Ohio. OSYSP is potent against enterohemorrhagic E. coli and is a candidate biocontrol agent for food and therapeutic applications. In this paper, we present the important genetic features of this phage based on its complete genome sequence.

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Goodall, Emily C. A., Ashley Robinson, Iain G. Johnston, Sara Jabbari, Keith A. Turner, Adam F. Cunningham, Peter A. Lund, Jeffrey A. Cole, and Ian R. Henderson. "The Essential Genome of Escherichia coli K-12." mBio 9, no. 1 (February 20, 2018). http://dx.doi.org/10.1128/mbio.02096-17.

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ABSTRACTTransposon-directed insertion site sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries, and therefore, it remains unclear whether the two methodologies are comparable. To address this, a high-density transposon library was constructed inEscherichia coliK-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false-positive identification of essential genes, statistical data analysis included corrections for both gene length and genome length. Through this analysis, new essential genes and genes previously incorrectly designated essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Examples include short essential regions within genes, orientation-dependent effects, and fine-resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis data sets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry.IMPORTANCEIncentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. To identify essential genes inEscherichia coli, we constructed a transposon mutant library of unprecedented density. Initial automated analysis of the resulting data revealed many discrepancies compared to the literature. We now report more extensive statistical analysis supported by both literature searches and detailed inspection of high-density TraDIS sequencing data for each putative essential gene for theE. colimodel laboratory organism. This paper is important because it provides a better understanding of the essential genes ofE. coli, reveals the limitations of relying on automated analysis alone, and provides a new standard for the analysis of TraDIS data.

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Mehershahi, Kurosh S., and Swaine L. Chen. "Complete Genome Sequence of the Uropathogenic Escherichia coli Strain NU14." Genome Announcements 5, no. 18 (May 4, 2017). http://dx.doi.org/10.1128/genomea.00306-17.

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ABSTRACT Escherichia coli is the most common bacterium causing urinary tract infections in humans. We report here the complete genome sequence of the uropathogenic Escherichia coli strain NU14, a clinical pyelonephritis isolate used for studying pathogenesis.

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Castro, Vinicius Silva, Eduardo Eustáquio de Souza Figueiredo, Tim McAllister, Robin King, Tim Reuter, Rodrigo Ortega Polo, Carlos Adam Conte, and Kim Stanford. "Whole-Genome Draft Assemblies of Difficult-to-Classify Escherichia coli O157 and Non-O157 Isolates from Feces of Canadian Feedlot Cattle." Microbiology Resource Announcements 9, no. 15 (April 9, 2020). http://dx.doi.org/10.1128/mra.00168-20.

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Forty-eight Escherichia coli strains were chosen due to variable detection of stx or serogroup by PCR. Although all strains were initially determined to be Shiga toxin-producing Escherichia coli (STEC), their genomes revealed 11 isolates carrying stx 1a, stx 1b, stx 2a, and/or stx 2b. Assembled genome sizes varied between 4,667,418 and 5,556,121 bp, with N 50 values between 79,648 and 294,166 bp and G+C contents between 50.

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