scholarly journals Accessory DNA in the Genomes of Representatives of the Escherichia coli Reference Collection

1999 ◽  
Vol 181 (8) ◽  
pp. 2548-2554 ◽  
Author(s):  
Ana Hurtado ◽  
Francisco Rodríguez-Valera
Keyword(s):  
Escherichia Coli ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
The Other ◽  
Rna Helicases ◽  
Significant Similarity ◽  
E Coli ◽  
Reference Collection ◽  
Different Strains ◽  
K 12

ABSTRACT Different strains of the Escherichia coli reference collection (ECOR) differ widely in chromosomal size. To analyze the nature of the differential gene pool carried by different strains, we have followed an approach in which random amplified polymorphic DNA (RAPD) was used to generate several PCR fragments. Those present in some but not all the strains were screened by hybridization to assess their distribution throughout the ECOR collection. Thirteen fragments with various degrees of occurrence were sequenced. Three of them corresponded to RAPD markers of widespread distribution. Of these, two were housekeeping genes shown by hybridization to be present in all theE. coli strains and in Salmonella enterica LT2; the third fragment contained a paralogous copy of dnaK with widespread, but not global, distribution. The other 10 RAPD markers were found in only a few strains. However, hybridization results demonstrated that four of them were actually present in a large selection of the ECOR collection (between 42 and 97% of the strains); three of these fragments contained open reading frames associated with phages or plasmids known in E. coli K-12. The remaining six fragments were present in only between one and four strains; of these, four fragments showed no similarity to any sequence in the databases, and the other two had low but significant similarity to a protein involved in the Klebsiella capsule synthesis and to RNA helicases of archaeal genomes, respectively. Their percent GC, dinucleotide content, and codon adaptation index suggested an exogenous origin by horizontal transfer. These results can be interpreted as reflecting the presence of a large pool of strain-specific genes, whose origin could be outside the species boundaries.

scholarly journals Molecular Characterization of Commensal Escherichia coli Adapted to Different Compartments of the Porcine Gastrointestinal Tract

2012 ◽  
Vol 78 (19) ◽  
pp. 6799-6803 ◽  
Author(s):  
Sam Abraham ◽  
David M. Gordon ◽  
James Chin ◽  
Huub J. M. Brouwers ◽  
Peter Njuguna ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gastrointestinal Tract ◽  
Random Amplified Polymorphic Dna ◽  
Content Type ◽  
E Coli ◽  
Plasmid Replicon ◽  
Different Strains ◽  
Different Characteristics

ABSTRACTThe role ofEscherichia colias a pathogen has been the focus of considerable study, while much less is known about it as a commensal and how it adapts to and colonizes different environmental niches within the mammalian gut. In this study, we characterizeEscherichia coliorganisms (n= 146) isolated from different regions of the intestinal tracts of eight pigs (dueodenum, ileum, colon, and feces). The isolates were typed using the method of random amplified polymorphic DNA (RAPD) and screened for the presence of bacteriocin genes and plasmid replicon types. Molecular analysis of variance using the RAPD data showed thatE. coliisolates are nonrandomly distributed among different gut regions, and that gut region accounted for 25% (P< 0.001) of the observed variation among strains. Bacteriocin screening revealed that a bacteriocin gene was detected in 45% of the isolates, with 43% carrying colicin genes and 3% carrying microcin genes. Of the bacteriocins observed (H47, E3, E1, E2, E7, Ia/Ib, and B/M), the frequency with which they were detected varied with respect to gut region for the colicins E2, E7, Ia/Ib, and B/M. The plasmid replicon typing gave rise to 25 profiles from the 13 Inc types detected. Inc F types were detected most frequently, followed by Inc HI1 and N types. Of the Inc types detected, 7 were nonrandomly distributed among isolates from the different regions of the gut. The results of this study indicate that not only may the different regions of the gastrointestinal tract harbor different strains ofE. colibut also that strains from different regions have different characteristics.

scholarly journals Quorum-Sensing Escherichia coli Regulator A: a Regulator of the LysR Family Involved in the Regulation of the Locus of Enterocyte Effacement Pathogenicity Island in Enterohemorrhagic E. coli

2002 ◽  
Vol 70 (6) ◽  
pp. 3085-3093 ◽  
Author(s):  
Vanessa Sperandio ◽  
Caiyi C. Li ◽  
James B. Kaper
Keyword(s):  
Escherichia Coli ◽  
Quorum Sensing ◽  
Type Iii Secretion ◽  
Pathogenicity Island ◽  
The Other ◽  
E Coli ◽  
Type Iii ◽  
Enterocyte Effacement ◽  
K 12 ◽  
Lysr Family

ABSTRACT The locus of enterocyte effacement (LEE) is a chromosomal pathogenicity island that encodes the proteins involved in the formation of the attaching and effacing lesions by enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC). The LEE comprises 41 open reading frames organized in five major operons, LEE1, LEE2, LEE3, tir (LEE5), and LEE4, which encode a type III secretion system, the intimin adhesin, the translocated intimin receptor (Tir), and other effector proteins. The first gene of LEE1 encodes the Ler regulator, which activates all the other genes within the LEE. We previously reported that the LEE genes were activated by quorum sensing through Ler (V. Sperandio, J. L. Mellies, W. Nguyen, S. Shin, and J. B. Kaper, Proc. Natl. Acad. Sci. USA 96:15196-15201, 1999). In this study we report that a putative regulator in the E. coli genome is itself activated by quorum sensing. This regulator is encoded by open reading frame b3243; belongs to the LysR family of regulators; is present in EHEC, EPEC, and E. coli K-12; and shares homology with the AphB and PtxR regulators of Vibrio cholerae and Pseudomonas aeruginosa, respectively. We confirmed the activation of b3243 by quorum sensing by using transcriptional fusions and renamed this regulator quorum-sensing E. coli regulator A (QseA). We observed that QseA activated transcription of ler and therefore of the other LEE genes. An EHEC qseA mutant had a striking reduction of type III secretion activity, which was complemented when qseA was provided in trans. Similar results were also observed with a qseA mutant of EPEC. The QseA regulator is part of the regulatory cascade that regulates EHEC and EPEC virulence genes by quorum sensing.

Effect of ozone on prophage induction in different strains of Escherichia coli K-12 lysogenic for lambda

1984 ◽  
Vol 26 (6) ◽  
pp. 706-709 ◽  
Author(s):  
Pierre L'Hérault ◽  
Young Sup Chung
Keyword(s):  
Escherichia Coli ◽  
Ultraviolet Light ◽  
Lytic Cycle ◽  
Prophage Induction ◽  
E Coli ◽  
Different Strains ◽  
K 12 ◽  
Lambda Prophage

Ozone was tested for its effect upon induction of lambda prophage in two different strains of Escherichia coli K-12. Based on the induction index and when compared to ultraviolet light, ozone appeared to be a weak, if any at all, inducer of the lytic cycle in E. coli. This is in agreement with other studies which have suggested that this agent is a weak inducer of the SOS functions.Key words: SOS functions, ultraviolet light, mutagen, ozone.

scholarly journals Activation of Prophage eib Genes for Immunoglobulin-Binding Proteins by Genes from the IbrAB Genetic Island of Escherichia coli ECOR-9

2002 ◽  
Vol 184 (13) ◽  
pp. 3640-3648 ◽  
Author(s):  
Carol H. Sandt ◽  
James E. Hopper ◽  
Charles W. Hill
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Phylogenetic Group ◽  
The Other ◽  
Overlapping Genes ◽  
Left Boundary ◽  
E Coli ◽  
Genome Homology ◽  
K 12 ◽  
Immunoglobulin Binding

ABSTRACT Four distinct Escherichia coli immunoglobulin-binding (eib) genes, each of which encodes a surface-exposed protein that binds immunoglobulins in a nonimmune manner, are carried by separate prophages in E. coli reference (ECOR) strain ECOR-9. Each eib gene was transferred to test E. coli strains, both in the form of multicopy recombinant plasmids and as lysogenized prophage. The derived lysogens express little or no Eib protein, in sharp contrast to the parental lysogen, suggesting that ECOR-9 has an expression-enhancing activity that the derived lysogens lack. Supporting this hypothesis, we cloned from ECOR-9 overlapping genes, ibrA and ibrB (designation is derived from “immunoglobulin-binding regulator”), which together activated eib expression in the derived lysogens. The proteins encoded by ibrA and ibrB are very similar to uncharacterized proteins encoded by genes of Salmonella enterica serovar Typhi and E. coli O157:H7 (in a prophage-like element of the Sakai strain and in two O islands of strain EDL933). The genomic segment containing ibrA and ibrB has been designated the IbrAB island. It contains regions of homology to the Shiga toxin-converting prophage, Stx2, as well as genes homologous to phage antirepressor genes. The left boundary between the IbrAB island and the chromosomal framework is located near min 35.8 of the E. coli K-12 genome. Homology to IbrAB was found in certain other ECOR strains, including the other five eib-positive strains and most strains of the phylogenetic group B2. Sequencing of a 1.1-kb portion of ibrAB revealed that the other eib-positive strains diverge by ≤0.1% from ECOR-9, whereas eib-negative ECOR-47 diverges by 16%.

scholarly journals Phosphoethanolamine substitution in the lipid A of Escherichia coli O157 : H7 and its association with PmrC

Microbiology ◽  
2006 ◽  
Vol 152 (3) ◽  
pp. 657-666 ◽  
Author(s):  
Sang-Hyun Kim ◽  
Wenyi Jia ◽  
Valeria R. Parreira ◽  
Russell E. Bishop ◽  
Carlton L. Gyles
Keyword(s):  
Escherichia Coli ◽  
Copy Number ◽  
Lipid A ◽  
High Copy Number ◽  
Peptide Antibiotics ◽  
Significant Similarity ◽  
E Coli ◽  
Copy Number Plasmid ◽  
High Copy Number Plasmid ◽  
K 12

This study shows that lipid A of Escherichia coli O157 : H7 differs from that of E. coli K-12 in that it has a phosphoform at the C-1 position, which is distinctively modified by a phosphoethanolamine (PEtN) moiety, in addition to the diphosphoryl form. The pmrC gene responsible for the addition of PEtN to the lipid A of E. coli O157 : H7 was inactivated and the changes in lipid A profiles were assessed. The pmrC null mutant still produced PEtN-modified lipid A species, albeit in a reduced amount, indicating that PmrC was not the only enzyme that could be used to add PEtN to lipid A. Natural PEtN substitution was shown to be present in the lipid A of other serotypes of enterohaemorrhagic E. coli and absent from the lipid A of E. coli K-12. However, the cloned pmrC O157 gene in a high-copy-number plasmid generated a large amount of PEtN-substituted lipid A species in E. coli K-12. The occurrence of PEtN-substituted lipid A species was associated with a slight increase in the MICs of cationic peptide antibiotics, suggesting that the lipid A modification with PEtN would be beneficial for survival of E. coli O157 : H7 in certain environmental niches. However, PEtN substitution in the lipid A profiles was not detected when putative inner-membrane proteins (YhbX/YbiP/YijP/Ecf3) that show significant similarity with PmrC in amino acid sequence were expressed from high-copy-number plasmids in E. coli K-12. This suggests that these potential homologues are not responsible for the addition of PEtN to lipid A in the pmrC mutant of E. coli O157 : H7. When cells were treated with EDTA, the amount of palmitoylated lipid A from the cells carrying a high-copy-number plasmid clone of pmrC O157 that resulted in significant increase of PEtN substitution was unchanged compared with cells without PEtN substitution, suggesting that the PEtN moiety substituted in lipid A does not compensate for the loss of divalent cations required for bridging neighbouring lipid A molecules.

scholarly journals A Novel Putrescine Importer Required for Type 1 Pili-driven Surface Motility Induced by Extracellular Putrescine in Escherichia coli K-12

2011 ◽  
Vol 286 (12) ◽  
pp. 10185-10192 ◽  
Author(s):  
Shin Kurihara ◽  
Hideyuki Suzuki ◽  
Mayu Oshida ◽  
Yoshimi Benno
Keyword(s):  
Escherichia Coli ◽  
Plasmid Vector ◽  
The Other ◽  
Gene Deletions ◽  
E Coli ◽  
Type 1 Pili ◽  
Transport Assay ◽  
Surface Motility ◽  
K 12

Recently, many studies have reported that polyamines play a role in bacterial cell-to-cell signaling processes. The present study describes a novel putrescine importer required for induction of type 1 pili-driven surface motility. The surface motility of the Escherichia coli ΔspeAB ΔspeC ΔpotABCD strain, which cannot produce putrescine and cannot import spermidine from the medium, was induced by extracellular putrescine. Introduction of the gene deletions for known polyamine importers (ΔpotE, ΔpotFGHI, and ΔpuuP) or a putative polyamine importer (ΔydcSTUV) into the ΔspeAB ΔspeC ΔpotABCD strain did not affect putrescine-induced surface motility. The deletion of yeeF, an annotated putative putrescine importer, in the ΔspeAB ΔspeC ΔpotABCD ΔydcSTUV strain abolished surface motility in putrescine-supplemented medium. Complementation of yeeF by a plasmid vector restored surface motility. The surface motility observed in the present study was abolished by the deletion of fimA, suggesting that the surface motility is type 1 pili-driven. A transport assay using the yeeF+ or ΔyeeF strains revealed that YeeF is a novel putrescine importer. The Km of YeeF (155 μm) is 40 to 300 times higher than that of other importers reported previously. On the other hand, the Vmax of YeeF (9.3 nmol/min/mg) is comparable to that of PotABCD, PotFGHI, and PuuP. The low affinity of YeeF for putrescine may allow E. coli to sense the cell density depending on the concentration of extracellular putrescine.

scholarly journals DELETION AND AMBER MUTANTS OF fla LOCI IN ESCHERICHIA COLI K-12

Genetics ◽  
1976 ◽  
Vol 84 (3) ◽  
pp. 403-421
Author(s):  
Hisato Kondoh ◽  
Haruo Ozeki
Keyword(s):  
Escherichia Coli ◽  
High Temperature ◽  
Genetic Map ◽  
Screening Method ◽  
The Other ◽  
Rapid Screening ◽  
E Coli ◽  
Flagellar Filament ◽  
Rapid Screening Method ◽  
K 12

ABSTRACT A rapid screening method for amber fla mutants of E. coli was devised and many mutants were obtained. In addition, strains with deletions of the fla genes in the his-uvrC region were isolated from high-temperature survivors of a λcI857 lysogen in which the prophage is located between his and fla. Utilizing these mutants, eleven fla genes (I-XI) and one hag gene were identified in the his-uvrc region, in the following order: his-supD-I-II-(III, IV)-V-(VI, VII)-VIII-IX-hag-(X, XI)-uvrC. The fla genes X and XI and hag are located at about 42.5 min and the other fla genes at about 43.0 min on the E. coli genetic map (Bachmann, Low and Taylor 1976). Mutants of fla gene X showed a slight sensitivity to chi phage, although they lack the flagellar filament.

scholarly journals Rhs Elements Comprise Three Subfamilies Which Diverged Prior to Acquisition by Escherichia coli

1998 ◽  
Vol 180 (16) ◽  
pp. 4102-4110 ◽  
Author(s):  
Yong-Dong Wang ◽  
Sheng Zhao ◽  
Charles W. Hill
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Analysis ◽  
Open Reading Frame ◽  
Large Protein ◽  
Rich Region ◽  
Reading Frame ◽  
E Coli ◽  
The Core ◽  
Reference Collection ◽  
K 12

ABSTRACT The Rhs elements are complex genetic composites widely spread among Escherichia coli isolates. One of their components, a 3.7-kb, GC-rich core, maintains a single open reading frame that extends the full length of the core and then 400 to 600 bp beyond into an AT-rich region. Whereas Rhs cores are homologous, core extensions from different elements are dissimilar. Two new Rhs elements from strains of the ECOR reference collection have been characterized. RhsG (from strain ECOR-11) maps to min 5.3, and RhsH (from strain ECOR-45) maps to min 32.8, where it lies in tandem with RhsE. Comparison of strain K-12 to ECOR-11 indicates that RhsGwas once present in but has been largely deleted from an ancestor of K-12. Phylogenetic analysis shows that the cores from eight known elements fall into three subfamilies, RhsA-B-C-F,RhsD-E, and RhsG-H. Cores from different subfamilies diverge 22 to 29%. Analysis of substitutions that distinguish between subfamilies shows that the origin of the ancestral core as well as the process of subfamily separation occurred in a GC-rich background. Furthermore, each subfamily independently passed from the GC-rich background to a less GC-rich background such asE. coli. A new example of core-extension shuffling provides the first example of exchange between cores of different subfamilies. A novel component of RhsE and RhsG,vgr, encodes a large protein distinguished by 18 to 19 repetitions of a Val-Gly dipeptide occurring with a eight-residue periodicity.

scholarly journals Correlation of Rhs elements with Escherichia coli population structure.

Genetics ◽  
1995 ◽  
Vol 141 (1) ◽  
pp. 15-24
Author(s):  
C W Hill ◽  
G Feulner ◽  
M S Brody ◽  
S Zhao ◽  
A B Sadosky ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Open Reading Frame ◽  
Clonal Structure ◽  
Reading Frame ◽  
E Coli ◽  
Sequence Identity ◽  
Reference Collection ◽  
K 12 ◽  
Recent Variation ◽  
Fourth Member

Abstract The Rhs family of composite genetic elements was assessed for variation among independent Escherichia coli strains of the ECOR reference collection. The location and content of the RhsA-B-C-F subfamily correlates highly with the clonal structure of the ECOR collection. This correlation exists at several levels: the presence of Rhs core homology in the strain, the location of the Rhs elements present, and the identity of the Rhs core-extensions associated with each element. A provocative finding was that an identical 1518-bp segment, covering core-extension-b1 and its associated downstream open reading frame, is present in two distinct clonal groups, but in association with different Rhs elements. The sequence identity of this segment when contrasted with the divergence of other chromosomal segments suggests that shuffling of Rhs core extensions has been a relatively recent variation. Nevertheless the copies of core-extension-b1 were placed within the respective Rhs elements before the emergence of the clonal groups. In the course of this analysis, two new Rhs elements absent from E. coli K-12 were discovered: RhsF, a fourth member of the RhsA-B-C-F subfamily, and RhsG, the prototype of a third Rhs subfamily.

scholarly journals Chromosomal Dynamism in Progeny of Outbreak-Related Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:NM

2006 ◽  
Vol 72 (3) ◽  
pp. 1900-1909 ◽  
Author(s):  
Martina Bielaszewska ◽  
Rita Prager ◽  
Wenlan Zhang ◽  
Alexander W. Friedrich ◽  
Alexander Mellmann ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Enterohemorrhagic Escherichia Coli ◽  
Outbreak Strain ◽  
E Coli ◽  
Shiga Toxin 2 ◽  
Uremic Syndrome ◽  
Sporadic Cases ◽  
Different Strains ◽  
K 12

ABSTRACT Sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:NM (nonmotile) is a unique clone that causes outbreaks of hemorrhagic colitis and hemolytic-uremic syndrome. In well-defined clusters of cases, we have observed significant variability in pulsed-field gel electrophoresis (PFGE) patterns which could indicate coinfection by different strains. An analysis of randomly selected progeny colonies of an outbreak strain after subcultivation demonstrated that they displayed either the cognate PFGE outbreak pattern or one of four additional patterns and were <89% similar. These profound alterations were associated with changes in the genomic position of one of two Shiga toxin 2-encoding genes (stx 2) in the outbreak strain or with the loss of this gene. The two stx 2 alleles in the outbreak strain were identical but were flanked with phage-related sequences with only 77% sequence identity. Neither of these phages produced plaques, but one lysogenized E. coli K-12 and integrated in yecE in the lysogens and the wild-type strain. The presence of two stx 2 genes which correlated with increased production of Stx2 in vitro but not with the clinical outcome of infection was also found in 14 (21%) of 67 SF EHEC O157:NM isolates from sporadic cases of human disease. The variability of PFGE patterns for the progeny of a single colony must be considered when interpreting PFGE patterns in SF EHEC O157-associated outbreaks.

Sign in / Sign up

Export Citation Format

Share Document