scholarly journals Closed Genome Sequence of Escherichia coli K-12 Group Strain C600

2019 ◽  
Vol 8 (2) ◽  
Author(s):  
Anna Allué-Guardia ◽  
Emmanuel C. Nyong ◽  
Sara S. K. Koenig ◽  
Sean M. Vargas ◽  
James L. Bono ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Laboratory Strain ◽  
Culture Collection ◽  
Content Type ◽  
Bacterial Physiology ◽  
E Coli ◽  
Molecular Microbiology ◽  
K 12 ◽  
Group Strain

Escherichia coli strain C600 is a prototypical K-12 derived laboratory strain which has been broadly used for molecular microbiology and bacterial physiology studies since its isolation in 1954. Here, we present the closed genome sequence of E. coli strain C600, retrieved from the American Type Culture Collection (ATCC 23724).

scholarly journals Complete Genome Sequence of Escherichia coli J53, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Yasufumi Matsumura ◽  
Gisele Peirano ◽  
Johann D. D. Pitout
Keyword(s):  
Escherichia Coli ◽  
Genetic Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Laboratory Strain ◽  
Content Type ◽  
E Coli ◽  
K 12

ABSTRACT We report here the complete genome sequence of Escherichia coli J53, which is used as a recipient in conjugation experiments and is a laboratory strain derived from E. coli K-12. This genome sequence will help in the development of a comprehensive genetic analysis of conjugative elements.

scholarly journals Complete Genome Sequence of Escherichia coli ME8067, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments

2018 ◽  
Vol 6 (25) ◽  
Author(s):  
Yasufumi Matsumura ◽  
Masaki Yamamoto ◽  
Satoshi Nakano ◽  
Miki Nagao
Keyword(s):  
Escherichia Coli ◽  
Genetic Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Laboratory Strain ◽  
Content Type ◽  
E Coli ◽  
K 12

ABSTRACT We report here the complete genome sequence of Escherichia coli ME8067, an azide-resistant laboratory strain used for conjugation experiments. The ME8067 genome was closely related to E. coli strain K-12 substrain W3110. This genome sequence will support further genetic analysis of conjugative elements.

scholarly journals Complete Genome Sequence of Escherichia coli Phage vB_EcoM_Alf5

2017 ◽  
Vol 5 (20) ◽  
Author(s):  
Laurynas Alijošius ◽  
Eugenijus Šimoliūnas ◽  
Laura Kaliniene ◽  
Rolandas Meškys ◽  
Lidija Truncaitė
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Molecular Level ◽  
Content Type ◽  
E Coli ◽  
Functional Studies ◽  
K 12 ◽  
Escherichia Coli Phage

ABSTRACT Here, we announce the complete genome sequence of the Escherichia coli myophage vB_EcoM_Alf5 belonging to the genus Felixo1virus, whose members have not been comprehensively studied at the molecular level. Phage vB_EcoM_Alf5 infects E. coli K-12-derived laboratory strains and therefore is well suited for functional studies.

scholarly journals Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain ATCC 43888

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Gaylen A. Uhlich ◽  
George C. Paoli ◽  
Xinmin Zhang ◽  
Elisa Andreozzi
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Culture Collection ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Strain Atcc ◽  
Content Type ◽  
E Coli ◽  
Fecal Isolate ◽  
Reduced Toxicity

Escherichia coli serotype O157:H7 strain ATCC 43888 is a Shiga toxin-deficient human fecal isolate. Due to its reduced toxicity and its availability from a curated culture collection, the strain has been used extensively in applied research studies. Here, we report the Illumina-corrected PacBio whole-genome sequence of E. coli O157:H7 strain ATCC 43888.

scholarly journals Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798)

2017 ◽  
Vol 5 (27) ◽  
Author(s):  
Daniela Dimitrova ◽  
Kathleen C. Engelbrecht ◽  
Catherine Putonti ◽  
David W. Koenig ◽  
Alan J. Wolfe
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
F Plasmid ◽  
Content Type ◽  
E Coli ◽  
K 12

ABSTRACT Here, we present the draft genome sequence of Escherichia coli ATCC 10798. E. coli ATCC 10798 is a K-12 strain, one of the most well-studied model microorganisms. The size of the genome was 4,685,496 bp, with a G+C content of 50.70%. This assembly consists of 62 contigs and the F plasmid.

scholarly journals Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database

2021 ◽  
Author(s):  
Donovan H Parks ◽  
Maria Chuvochina ◽  
Peter R Reeves ◽  
Scott A Beatson ◽  
Philip Hugenholtz
Keyword(s):  
Escherichia Coli ◽  
Type Strain ◽  
Shigella Flexneri ◽  
Laboratory Strain ◽  
Single Species ◽  
Species Definition ◽  
E Coli ◽  
Shigella Species ◽  
K 12 ◽  
Common Laboratory

Members of the genus Shigella have high genomic similarity to Escherichia coli and are often considered to be atypical members of this species. In an attempt to retain Shigella species as recognizable entities, they were reclassified as Escherichia species in the Genome Taxonomy Database (GTDB) using an operational average nucleotide identity (ANI)-based approach nucleated around type strains. This resulted in nearly 80% of E. coli genomes being reclassified to new species including the common laboratory strain E. coli K-12 (to 'E. flexneri') because it is more closely related to the type strain of Shigella flexneri than it is to the type strain of E. coli. Here we resolve this conundrum by treating Shigella species as later heterotypic synonyms of E. coli, present evidence supporting this reclassification, and show that assigning E. coli/Shigella strains to a single species is congruent with the GTDB-adopted genomic species definition.

scholarly journals Molecular Control of Sucrose Utilization in Escherichia coli W, an Efficient Sucrose-Utilizing Strain

2012 ◽  
Vol 79 (2) ◽  
pp. 478-487 ◽  
Author(s):  
Suriana Sabri ◽  
Lars K. Nielsen ◽  
Claudia E. Vickers
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Good Growth ◽  
Knockout Mutant ◽  
Sucrose Transport ◽  
Molecular Control ◽  
Content Type ◽  
E Coli ◽  
K 12 ◽  
Sucrose Utilization

ABSTRACTSucrose is an industrially important carbon source for microbial fermentation. Sucrose utilization inEscherichia coli, however, is poorly understood, and most industrial strains cannot utilize sucrose. The roles of the chromosomally encoded sucrose catabolism (csc) genes inE. coliW were examined by knockout and overexpression experiments. At low sucrose concentrations, thecscgenes are repressed and cells cannot grow. Removal of either the repressor protein (cscR) or the fructokinase (cscK) gene facilitated derepression. Furthermore, combinatorial knockout ofcscRandcscKconferred an improved growth rate on low sucrose. The invertase (cscA) and sucrose transporter (cscB) genes are essential for sucrose catabolism inE. coliW, demonstrating that no other genes can provide sucrose transport or inversion activities. However,cscKis not essential for sucrose utilization. Fructose is excreted into the medium by thecscK-knockout strain in the presence of high sucrose, whereas at low sucrose (when carbon availability is limiting), fructose is utilized by the cell. Overexpression ofcscA,cscAK, orcscABcould complement the WΔcscRKABknockout mutant or confer growth on a K-12 strain which could not naturally utilize sucrose. However, phenotypic stability and relatively good growth rates were observed in the K-12 strain only when overexpressingcscAB, and full growth rate complementation in WΔcscRKABalso requiredcscAB. Our understanding of sucrose utilization can be used to improveE. coliW and engineer sucrose utilization in strains which do not naturally utilize sucrose, allowing substitution of sucrose for other, less desirable carbon sources in industrial fermentations.

scholarly journals Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

2012 ◽  
Vol 57 (1) ◽  
pp. 189-195 ◽  
Author(s):  
Migla Miskinyte ◽  
Isabel Gordo
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Resistance Mutation ◽  
Fitness Cost ◽  
Resistance Mutations ◽  
Content Type ◽  
E Coli ◽  
Fitness Effects ◽  
K 12

ABSTRACTMutations causing antibiotic resistance usually incur a fitness cost in the absence of antibiotics. The magnitude of such costs is known to vary with the environment. Little is known about the fitness effects of antibiotic resistance mutations when bacteria confront the host's immune system. Here, we study the fitness effects of mutations in therpoB,rpsL, andgyrAgenes, which confer resistance to rifampin, streptomycin, and nalidixic acid, respectively. These antibiotics are frequently used in the treatment of bacterial infections. We measured two important fitness traits—growth rate and survival ability—of 12Escherichia coliK-12 strains, each carrying a single resistance mutation, in the presence of macrophages. Strikingly, we found that 67% of the mutants survived better than the susceptible bacteria in the intracellular niche of the phagocytic cells. In particular, allE. colistreptomycin-resistant mutants exhibited an intracellular advantage. On the other hand, 42% of the mutants incurred a high fitness cost when the bacteria were allowed to divide outside of macrophages. This study shows that single nonsynonymous changes affecting fundamental processes in the cell can contribute to prolonged survival ofE. coliin the context of an infection.

scholarly journals Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5α

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Jingchao Chen ◽  
Yi Li ◽  
Kun Zhang ◽  
Hailei Wang
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Genome Sequence ◽  
Resistant Strain ◽  
Resistance Mechanism ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
T4 Bacteriophage

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 .

scholarly journals Flexible Metabolism and Suppression of Latent Enzymes Are Important forEscherichia coliAdaptation to Diverse Environments within the Host

2019 ◽  
Vol 201 (16) ◽  
Author(s):  
Christopher J. Alteri ◽  
Stephanie D. Himpsl ◽  
Allyson E. Shea ◽  
Harry L. T. Mobley
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Pyruvate Kinase ◽  
Tricarboxylic Acid Cycle ◽  
Financial Burden ◽  
Content Type ◽  
Bacterial Physiology ◽  
E Coli ◽  
Growth Requirements ◽  
Tract Infections

ABSTRACTBacterial metabolism is necessary for adaptation to the host microenvironment. Flexible metabolic pathways allow uropathogenicEscherichia coli(UPEC) to harmlessly reside in the human intestinal tract and cause disease upon extraintestinal colonization.E. coliintestinal colonization requires carbohydrates as a carbon source, while UPEC extraintestinal colonization requires gluconeogenesis and the tricarboxylic acid cycle. UPEC containing disruptions in two irreversible glycolytic steps involving 6-carbon (6-phosphofructokinase;pfkA) and 3-carbon (pyruvate kinase;pykA) substrates have no fitness defect during urinary tract infection (UTI); however, both reactions are catalyzed by isozymes: 6-phosphofructokinases Pfk1 and Pfk2, encoded bypfkAandpfkB, and pyruvate kinases Pyk II and Pyk I, encoded bypykAandpykF. UPEC strains lacking one or both phosphofructokinase-encoding genes (pfkBandpfkA pfkB) and strains lacking one or both pyruvate kinase genes (pykFandpykA pykF) were investigated to determine their regulatory roles in carbon flow during glycolysis by examining their fitness during UTI andin vitrogrowth requirements. Loss of a single phosphofructokinase-encoding gene has no effect on fitness, while thepfkA pfkBdouble mutant outcompeted the parental strain in the bladder. A defect in bladder and kidney colonization was observed with loss ofpykF, while loss ofpykAresulted in a fitness advantage. ThepykA pykFmutant was indistinguishable from wild-typein vivo, suggesting that the presence of Pyk II rather than the loss of Pyk I itself is responsible for the fitness defect in thepykFmutant. These findings suggest thatE. colisuppresses latent enzymes to survive in the host urinary tract.IMPORTANCEUrinary tract infections are the most frequently diagnosed urologic disease, with uropathogenicEscherichia coli(UPEC) infections placing a significant financial burden on the health care system by generating more than two billion dollars in annual costs. This, in combination with steadily increasing antibiotic resistances to present day treatments, necessitates the discovery of new antimicrobial agents to combat these infections. By broadening our scope beyond the study of virulence properties and investigating bacterial physiology and metabolism, we gain a better understanding of how pathogens use nutrients and compete within host microenvironments, enabling us to cultivate new therapeutics to exploit and target pathogen growth requirements in a specific host environment.

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