Escherichia coli interactions with Acanthamoeba: a symbiosis with environmental and clinical implications

The ability of Acanthamoeba to feed on Gram-negative bacteria, as well as to harbour potential pathogens, such as Legionella pneumophila, Coxiella burnetii, Pseudomonas aeruginosa, Vibrio cholerae, Helicobacter pylori, Listeria monocytogenes and Mycobacterium avium, suggest that both amoebae and bacteria are involved in complex interactions, which may play important roles in the environment and in human health. In this study, Acanthamoeba castellanii (a keratitis isolate belonging to the T4 genotype) was used and its interactions with Escherichia coli (strain K1, a cerebrospinal fluid isolate from a meningitis patient, O18 : K1 : H7, and a K-12 laboratory strain, HB101) were studied. The invasive K1 isolate exhibited a significantly higher association with A. castellanii than the non-invasive K-12 isolate. Similarly, K1 showed significantly increased invasion and/or uptake by A. castellanii in gentamicin protection assays than the non-invasive K-12. Using several mutants derived from K1, it was observed that outer-membrane protein A (OmpA) and LPS were crucial bacterial determinants responsible for E. coli K1 interactions with A. castellanii. Once inside the cell, E. coli K1 remained viable and multiplied within A. castellanii, while E. coli K-12 was killed. Again, OmpA and LPS were crucial for E. coli K1 intracellular survival in A. castellanii. In conclusion, these findings suggest that E. coli K1 interactions with A. castellanii are carefully regulated by the virulence of E. coli.

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

10.1101/2021.09.22.461432 ◽

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.

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Affinity Isolation and I-DIRT Mass Spectrometric Analysis of the Escherichia coli O157:H7 Sakai RNA Polymerase Complex

Journal of Bacteriology ◽

10.1128/jb.01599-07 ◽

2007 ◽

Vol 190 (4) ◽

pp. 1284-1289 ◽

Cited By ~ 14

Author(s):

David J. Lee ◽

Stephen J. W. Busby ◽

Lars F. Westblade ◽

Brian T. Chait

Keyword(s):

Escherichia Coli ◽

Rna Polymerase ◽

Transcription Initiation ◽

Laboratory Strain ◽

Effector Proteins ◽

Spectrometric Analysis ◽

Isolation Technique ◽

E Coli ◽

Affinity Isolation ◽

K 12

ABSTRACT Bacteria contain a single multisubunit RNA polymerase that is responsible for the synthesis of all RNA. Previous studies of the Escherichia coli K-12 laboratory strain identified a group of effector proteins that interact directly with RNA polymerase to modulate the efficiency of transcription initiation, elongation, or termination. Here we used a rapid affinity isolation technique to isolate RNA polymerase from the pathogenic Escherichia coli strain O157:H7 Sakai. We analyzed the RNA polymerase enzyme complex using mass spectrometry and identified associated proteins. Although E. coli O157:H7 Sakai contains more than 1,600 genes not present in the K-12 strain, many of which are predicted to be involved in transcription regulation, all of the identified proteins in this study were encoded on the “core” E. coli genome.

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Functional analysis of deoxyhexose sugar utilization in Escherichia coli reveals fermentative metabolism under aerobic conditions

Applied and Environmental Microbiology ◽

10.1128/aem.00719-21 ◽

2021 ◽

Author(s):

Pierre Millard ◽

Julien Pérochon ◽

Fabien Letisse

Keyword(s):

Escherichia Coli ◽

Metabolic Flux ◽

Sugar Metabolism ◽

Laboratory Strain ◽

Flux Analysis ◽

Aerobic Growth ◽

Aerobic Conditions ◽

E Coli ◽

Metabolic Analysis ◽

K 12

L-rhamnose and L-fucose are the two main 6-deoxyhexoses Escherichia coli can use as carbon and energy sources. Deoxyhexose metabolism leads to the formation of lactaldehyde whose fate depends on oxygen availability. Under anaerobic conditions, lactaldehyde is reduced to 1,2-propanediol whereas under aerobic condition, it should be oxidised into lactate and then channelled into the central metabolism. However, although this all-or-nothing view is accepted in the literature, it seems overly simplistic since propanediol is also reported to be present in the culture medium during aerobic growth on L-fucose. To clarify the functioning of 6-deoxyhexose sugar metabolism, a quantitative metabolic analysis was performed to determine extra- and intracellular fluxes in E. coli K-12 MG1655 (a laboratory strain) and in E. coli Nissle 1917 (a human commensal strain) during anaerobic and aerobic growth on L-rhamnose and L-fucose. As expected, lactaldehyde is fully reduced to 1,2-propanediol in anoxic conditions allowing complete reoxidation of the NADH produced by glyceraldehyde-3-phosphate-dehydrogenase. We also found that net ATP synthesis is ensured by acetate production. More surprisingly, lactaldehyde is also primarily reduced into 1,2-propanediol under aerobic conditions. For growth on L-fucose, 13 C-metabolic flux analysis revealed a large excess of available energy, highlighting the need to better characterize ATP utilization processes. The probiotic E. coli Nissle 1917 strain exhibits similar metabolic traits, indicating that they are not the result of the K-12 strain’s prolonged laboratory use. IMPORTANCE E. coli ’s ability to survive, grow and colonize the gastrointestinal tract stems from its use of partially digested food and hydrolysed glycosylated proteins (mucins) from the intestinal mucus layer as substrates. These include L-fucose and L-rhamnose, two 6-deoxyhexose sugars, whose catabolic pathways have been established by genetic and biochemical studies. However, the functioning of these pathways has only partially been elucidated. Our quantitative metabolic analysis provides a comprehensive picture of 6-deoxyhexose sugar metabolism in E. coli under anaerobic and aerobic conditions. We found that 1,2-propanediol is a major by-product under both conditions, revealing the key role of fermentative pathways in 6-deoxyhexose sugar metabolism. This metabolic trait is shared by both E. coli strains studied here, a laboratory strain and a probiotic strain. Our findings add to our understanding of E. coli ’s metabolism and of its functioning in the bacterium’s natural environment.

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

Genome Announcements ◽

10.1128/genomea.00433-18 ◽

2018 ◽

Vol 6 (21) ◽

Cited By ~ 3

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.

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

Genome Announcements ◽

10.1128/genomea.00515-18 ◽

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.

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

Microbiology Resource Announcements ◽

10.1128/mra.01052-18 ◽

2019 ◽

Vol 8 (2) ◽

Cited By ~ 3

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).

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The effect of sucrose-induced osmotic stress on the sensitivity of Escherichia coli to bacteriocins

Canadian Journal of Microbiology ◽

10.1139/cjm-2019-0292 ◽

2019 ◽

Vol 65 (12) ◽

pp. 895-903 ◽

Cited By ~ 1

Author(s):

Tatyana Polyudova ◽

Daria Eroshenko ◽

Vladimir Korobov

Keyword(s):

Escherichia Coli ◽

Osmotic Stress ◽

Morphological Changes ◽

Sucrose Solution ◽

Gram Negative Bacteria ◽

Lytic Enzymes ◽

Gram Negative ◽

E Coli ◽

Cell Counts ◽

K 12

Bacteriocins are antimicrobial peptides, produced by Gram-positive bacteria such as lactococci and staphylococci, that have limited bactericidal action against Gram-negative bacteria. The aim of this paper was to study the sensitivity of three strains of Escherichia coli to bacteriocins: nisin (as Nisaplin®) and two staphylococcal peptides (warnerin and hominin) during sucrose-induced osmotic stress. We found that all peptides in a 0.3 g·mL−1 sucrose solution significantly reduced the number of viable E. coli. The most pronounced antibacterial effect was achieved by nisin against E. coli K-12 (3 log reduction). Slightly less bactericidal effects were observed with warnerin (1 mg·mL−1) and hominin (1 mg·mL−1) in sucrose solution. The lytic activity of staphylococcal peptides was detected by decreased optical density and viable cell counts. Moreover, it was confirmed by the increased amount of DNA and protein in the medium and the morphological changes detected by atomic force microscopy after 20 h of treatment. Zymographic analysis revealed the release of lytic enzymes from E. coli cells after treatment with staphylococcal peptides and sucrose. These results indicated that the antimicrobial action of peptides can be extended to Gram-negative bacteria via combination with high concentrations of sucrose.

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Synergistic Effects in Mixed Escherichia coli Biofilms: Conjugative Plasmid Transfer Drives Biofilm Expansion

Journal of Bacteriology ◽

10.1128/jb.188.10.3582-3588.2006 ◽

2006 ◽

Vol 188 (10) ◽

pp. 3582-3588 ◽

Cited By ~ 87

Author(s):

Andreas Reisner ◽

Brigitte M. Höller ◽

Søren Molin ◽

Ellen L. Zechner

Keyword(s):

Escherichia Coli ◽

Synergistic Effects ◽

Laboratory Strain ◽

Single Species ◽

Conjugative Plasmid ◽

Laboratory Model ◽

Detailed Knowledge ◽

E Coli ◽

K 12 ◽

Biofilm Development

ABSTRACT Bacterial biofilms, often composed of multiple species and genetically distinct strains, develop under complex influences of cell-cell interactions. Although detailed knowledge about the mechanisms underlying formation of single-species laboratory biofilms has emerged, little is known about the pathways governing development of more complex heterogeneous communities. In this study, we established a laboratory model where biofilm-stimulating effects due to interactions between genetically diverse strains of Escherichia coli were monitored. Synergistic induction of biofilm formation resulting from the cocultivation of 403 undomesticated E. coli strains with a characterized E. coli K-12 strain was detected at a significant frequency. The survey suggests that different mechanisms underlie the observed stimulation, yet synergistic development of biofilm within the subset of E. coli isolates (n = 56) exhibiting the strongest effects was most often linked to conjugative transmission of natural plasmids carried by the E. coli isolates (70%). Thus, the capacity of an isolate to promote the biofilm through cocultivation was (i) transferable to the K-12 strain, (ii) was linked with the acquisition of conjugation genes present initially in the isolate, and (iii) was inhibited through the presence in the cocultured K-12 strain of a related conjugative plasmid, presumably due to surface exclusion functions. Synergistic effects of cocultivation of pairs of natural isolates were also observed, demonstrating that biofilm promotion in this system is not dependent on the laboratory strain and that the described model system could provide relevant insights on mechanisms of biofilm development in natural E. coli populations.

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The Endophytic Lifestyle of Escherichia coli O157:H7: Quantification and Internal Localization in Roots

Phytopathology ◽

10.1094/phyto-08-12-0209-fi ◽

2013 ◽

Vol 103 (4) ◽

pp. 333-340 ◽

Cited By ~ 48

Author(s):

Kathryn M. Wright ◽

Sean Chapman ◽

Kara McGeachy ◽

Sonia Humphris ◽

Emma Campbell ◽

...

Keyword(s):

Escherichia Coli ◽

Bacterial Colonization ◽

Fresh Produce ◽

Foodborne Pathogen ◽

Laboratory Strain ◽

Escherichia Coli O157 ◽

Cortical Cells ◽

E Coli ◽

K 12 ◽

Internal Colonization

The foodborne pathogen Escherichia coli O157:H7 is increasingly associated with fresh produce (fruit and vegetables). Bacterial colonization of fresh produce plants can occur to high levels on the external tissue but bacteria have also been detected within plant tissue. However, questions remain about the extent of internalization, its molecular basis, and internal location of the bacteria. We have determined the extent of internalization of E. coli O157:H7 in live spinach and lettuce plants and used high-resolution microscopy to examine colony formation in roots and pathways to internalization. E. coli O157:H7 was found within internal tissue of both produce species. Colonization occurred within the apoplast between plant cells. Furthermore, colonies were detected inside the cell wall of epidermal and cortical cells of spinach and Nicotiana benthamiana roots. Internal colonization of epidermal cells resembled that of the phytopathogen Pectobacterium atrosepticum on potato. In contrast, only sporadic cells of the laboratory strain of E. coli K-12 were found on spinach, with no internal bacteria evident. The data extend previous findings that internal colonization of plants appears to be limited to a specific group of plant-interacting bacteria, including E. coli O157:H7, and demonstrates its ability to invade the cells of living plants.

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Functional analysis of deoxyhexose sugar utilization in Escherichia coli reveals fermentative metabolism under aerobic conditions

10.1101/2021.04.12.439581 ◽

2021 ◽

Author(s):

Pierre Millard ◽

Julien Pérochon ◽

Fabien Letisse

Keyword(s):

Escherichia Coli ◽

Metabolic Flux ◽

Sugar Metabolism ◽

Laboratory Strain ◽

Flux Analysis ◽

Aerobic Growth ◽

Aerobic Conditions ◽

E Coli ◽

Metabolic Analysis ◽

K 12

ABSTRACTL-rhamnose and L-fucose are the two main 6-deoxyhexoses Escherichia coli can use as carbon and energy sources. Deoxyhexose metabolism leads to the formation of lactaldehyde whose fate depends on oxygen availability. Under anaerobic conditions, lactaldehyde is reduced to 1,2-propanediol whereas under aerobic condition, it should be oxidised into lactate and then channelled into the central metabolism. However, although this all-or-nothing view is accepted in the literature, it seems overly simplistic since propanediol is also reported to be present in the culture medium during aerobic growth on L-fucose. To clarify the functioning of 6-deoxyhexose sugar metabolism, a quantitative metabolic analysis was performed to determine extra- and intracellular fluxes in E. coli K-12 MG1655 (a laboratory strain) and in E. coli Nissle 1917 (a human commensal strain) during anaerobic and aerobic growth on L-rhamnose and L-fucose. As expected, lactaldehyde is fully reduced to 1,2-propanediol in anoxic conditions allowing complete reoxidation of the NADH produced by glyceraldehyde-3-phosphate-dehydrogenase. We also found that net ATP synthesis is ensured by acetate production. More surprisingly, lactaldehyde is also primarily reduced into 1,2-propanediol under aerobic conditions. For growth on L-fucose, 13C-metabolic flux analysis revealed a large excess of available energy, highlighting the need to better characterize ATP utilization processes. The probiotic E. coli Nissle 1917 strain exhibits similar metabolic traits, indicating that they are not the result of the K-12 strain’s prolonged laboratory use.IMPORTANCEE. coli’s ability to survive, grow and colonize the gastrointestinal tract stems from its use of partially digested food and hydrolysed glycosylated proteins (mucins) from the intestinal mucus layer as substrates. These include L-fucose and L-rhamnose, two 6-deoxyhexose sugars, whose catabolic pathways have been established by genetic and biochemical studies. However, the functioning of these pathways has only partially been elucidated. Our quantitative metabolic analysis provides a comprehensive picture of 6-deoxyhexose sugar metabolism in E. coli under anaerobic and aerobic conditions. We found that 1,2-propanediol is a major by-product under both conditions, revealing the key role of fermentative pathways in 6-deoxyhexose sugar metabolism. This metabolic trait is shared by both E. coli strains studied here, a laboratory strain and a probiotic strain. Our findings add to our understanding of E. coli’s metabolism and of its functioning in the bacterium’s natural environment.

Download Full-text