scholarly journals Bacterial Interspersed Mosaic Elements (BIMEs) Are a Major Source of Sequence Polymorphism in Escherichia coli Intergenic Regions Including Specific Associations With a New Insertion Sequence

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 551-562 ◽  
Author(s):  
Sophie Bachellier ◽  
Jean-Marie Clément ◽  
Maurice Hofnung ◽  
Eric Gilson
Keyword(s):  
Escherichia Coli ◽  
Dna Sequences ◽  
Multiple Sequence ◽  
E Coli ◽  
Sequence Organization ◽  
Is Element ◽  
Integration Sites ◽  
Intergenic Regions ◽  
Natural Isolates ◽  
K 12

A significant fraction of Escherichia coli intergenic DNA sequences is composed of two families of repeated bacterial interspersed mosaic elements (BIME-1 and BIME-2). In this study, we determined the sequence organization of six intergenic regions in 51 E. coli and Shigella natural isolates. Each region contains a BIME in E. coli K-12. We found that multiple sequence variations are located within or near these BIMEs in the different bacteria. Events included excisions of a whole BIME-1, expansion/deletion within a BIME-2 and insertions of non-BIME sequences like the boxC repeat or a new IS element, named IS 1397. Remarkably, 14 out of 14 IS 1397 integration sites correspond to a BIME sequence, strongly suggesting that this IS element is specifically associated with BIMEs, and thus inserts only in extragenic regions. Unlike BIMEs, IS 1397 is not detected in all E. coli isolates. Possible relationships between the presence of this IS element and the evolution of BIMEs are discussed.

scholarly journals IS1397 Is Active for Transposition into the Chromosome of Escherichia coli K-12 and Inserts Specifically into Palindromic Units of Bacterial Interspersed Mosaic Elements

1999 ◽  
Vol 181 (22) ◽  
pp. 6929-6936 ◽  
Author(s):  
Jean-Marie Clément ◽  
Caroline Wilde ◽  
Sophie Bachellier ◽  
Patricia Lambert ◽  
Maurice Hofnung
Keyword(s):  
Escherichia Coli ◽  
Mobile Genetic Element ◽  
Basic Element ◽  
Genetic Element ◽  
Repeated Element ◽  
E Coli ◽  
Intergenic Regions ◽  
Natural Isolates ◽  
K 12

ABSTRACT We demonstrate that IS1397, a putative mobile genetic element discovered in natural isolates of Escherichia coli, is active for transposition into the chromosome of E. coliK-12 and inserts specifically into palindromic units, also called repetitive extragenic palindromes, the basic element of bacterial interspersed mosaic elements (BIMEs), which are found in intergenic regions of enterobacteria closely related to E. coli andSalmonella. We could not detect transposition onto a plasmid carrying BIMEs. This unprecedented specificity of insertion into a well-characterized chromosomal intergenic repeated element and its evolutionary implications are discussed.

Genes encoding osmoregulatory proline/glycine betaine transporters and the proline catabolic system are present and expressed in diverse clinical Escherichia coli isolates

1994 ◽  
Vol 40 (5) ◽  
pp. 397-402 ◽  
Author(s):  
Doreen E. Culham ◽  
Katherine S. Emmerson ◽  
Bonnie Lasby ◽  
Daniel Mamelak ◽  
Brian A. Steer ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Dna Sequences ◽  
Glycine Betaine ◽  
Clinical Isolates ◽  
E Coli ◽  
High Osmolality ◽  
Proline Catabolism ◽  
K 12 ◽  
Physiological Tests

Sixty-three clinical isolates identified as Escherichia coli, 30 from the human urinary tract and 33 derived from other human origins, were screened for proline/glycine betaine transporters similar to those that support proline catabolism and proline- or glycine betaine-based osmoregulation in E. coli K-12. Both molecular (DNA- and protein-based) analyses and physiological tests were performed. All tests were calibrated with E. coli K-12 derivatives from which genetic loci putP (encoding a proline transporter required for proline catabolism), proP, and (or) proU (loci encoding osmoregulatory proline/glycine betaine transporters) had been deleted. All clinical isolates showed both enhanced sensitivity to the toxic proline analogue azetidine-2-carboxylate on media of high osmolality and growth stimulation by glycine betaine in an artificial urine preparation of high osmolality. DNA sequences similar to the putP, proP, and proU loci of E. coli K-12 were detected by DNA amplification and (or) hybridization and protein specifically reactive with antibodies raised against the ProX protein of E. coli K-12 (a ProU constituent) was detected by western blotting in over 95% of the isolates. Two anomalous isolates were reclassified as non-E. coli on the basis of the API 20E series of tests. A protein immunochemically cross-reactive with the ProP protein of E. coli K-12 was also expressed by the clinical isolates. Since all three transporters were ubiquitous, no particular correlation between clinical origin and PutP, ProP, or ProU activity was observed. These data suggest that the transporters encoded in loci putP, proP, and proU perform housekeeping functions essential for the survival of E. coli cells in diverse habitats.Key words: osmoregulation, betaine transport, urinary tract infection, Escherichia coli.

scholarly journals CS5 Pilus Biosynthesis Genes from Enterotoxigenic Escherichia coli O115:H40

1999 ◽  
Vol 181 (18) ◽  
pp. 5847-5851 ◽  
Author(s):  
Thomas G. Duthy ◽  
Lothar H. Staendner ◽  
Paul A. Manning ◽  
Michael W. Heuzenroeder
Keyword(s):  
Escherichia Coli ◽  
Dna Sequences ◽  
Surface Expression ◽  
Open Reading Frames ◽  
Enterotoxigenic Escherichia Coli ◽  
Cell Surface Expression ◽  
E Coli ◽  
Pilus Biogenesis ◽  
K 12 ◽  
And Function

ABSTRACT We have sequenced the entire region of DNA required for the biosynthesis of CS5 pili from enterotoxigenic Escherichia coli O115:H40 downstream of the major subunit gene, designatedcsfA (for coli surface factor five A). Five more open reading frames (ORFs) (csfB, csfC,csfE, csfF, and csfD) which are transcribed in the same direction as the major subunit and are flanked by a number of insertion sequence regions have been identified. T7 polymerase-mediated overexpression of the cloned csf ORFs confirmed protein sizes based on the DNA sequences that encode them. The expression of only the csf region in E. coli K-12 resulted in the hemagglutination of human erythrocytes and the cell surface expression of CS5 pili, suggesting that the cluster contains all necessary information for CS5 pilus biogenesis and function.

scholarly journals Representational Difference Analysis between Afa/Dr Diffusely Adhering Escherichia coli and Nonpathogenic E. coli K-12

2002 ◽  
Vol 70 (10) ◽  
pp. 5503-5511 ◽  
Author(s):  
Anne-Beatrice Blanc-Potard ◽  
Colin Tinsley ◽  
Isabel Scaletsky ◽  
Chantal Le Bouguenec ◽  
Julie Guignot ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Sequences ◽  
Effector Proteins ◽  
Representational Difference Analysis ◽  
Transport Systems ◽  
Difference Analysis ◽  
E Coli ◽  
Tract Infections ◽  
K 12 ◽  
Specific Sequences

ABSTRACT Diffusely adhering Escherichia coli strains harboring Afa/Dr adhesins (Afa/Dr DAEC) have been associated with diarrhea and urinary tract infections (UTIs). The present work is the first extensive molecular study of a Afa/Dr DAEC strain using the representational difference analysis technique. We have searched for DNA sequences present in strain C1845, recovered from a diarrheagenic child, but absent from a nonpathogenic K-12 strain. Strain C1845 harbors part of a pathogenicity island (PAICFT073) and several iron transport systems found in other E. coli pathovars. We did not find genes encoding factors known to subvert host cell proteins, such as type III secretion system or effector proteins. Several C1845-specific sequences are homologous to putative virulence genes or show no homology with known sequences, and we have analyzed their distribution among Afa/Dr and non-Afa/Dr clinical isolates and among strains from the E. coli Reference Collection. Three C1845-specific sequences (MO30, S109, and S111) have a high prevalence (77 to 80%) among Afa/Dr strains and a low prevalence (12 to 23%) among non-Afa/Dr strains. In addition, our results indicate that strain IH11128, an Afa/Dr DAEC strain recovered from a patient with a UTI, is genetically closely related to strain C1845.

Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31)

Microbiology ◽  
2005 ◽  
Vol 151 (2) ◽  
pp. 385-398 ◽  
Author(s):  
Jana Hejnova ◽  
Ulrich Dobrindt ◽  
Radka Nemcova ◽  
Christophe Rusniok ◽  
Alojz Bomba ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multiplex Pcr ◽  
Gene Clusters ◽  
Coli Strain ◽  
Bac Clone ◽  
Sequence Comparisons ◽  
Multiple Sequence ◽  
E Coli ◽  
Gut Colonization ◽  
K 12

Colonization by the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31) has proved to be safe and efficient in the prophylaxis and treatment of nosocomial infections and diarrhoea of preterm and newborn infants in Czech paediatric clinics over the past three decades. In searching for traits contributing to this beneficial effect related to the gut colonization capacity of the strain, the authors have analysed its genome by DNA–DNA hybridization to E. coli K-12 (MG1655) genomic DNA arrays and to ‘Pathoarrays’, as well as by multiplex PCR, bacterial artificial chromosome (BAC) library cloning and shotgun sequencing. Four hundred and ten E. coli K-12 ORFs were absent from A0 34/86, while 72 out of 456 genes associated with pathogenicity islands of E. coli and Shigella were also detected in E. coli A0 34/86. Furthermore, extraintestinal pathogenic E. coli-related genes involved in iron uptake and adhesion were detected by multiplex PCR, and genes encoding the HlyA and cytotoxic necrotizing factor toxins, together with 21 genes of the uropathogenic E. coli 536 pathogenicity island II, were identified by analysis of 2304 shotgun and 1344 BAC clone sequences of A0 34/86 DNA. Multiple sequence comparisons identified 31 kb of DNA specific for E. coli A0 34/86; some of the genes carried by this DNA may prove to be implicated in the colonization capacity of the strain, enabling it to outcompete pathogens. Among 100 examined BAC clones roughly covering the A0 34/86 genome, one reproducibly conferred on the laboratory strain DH10B an enhanced capacity to persist in the intestine of newborn piglets. Sequencing revealed that this BAC clone carried gene clusters encoding gluconate and mannonate metabolism, adhesion (fim), invasion (ibe) and restriction/modification functions. Hence, the genome of this clinically safe and highly efficient colonizer strain appears to harbour many ‘virulence-associated’ genes. These results highlight the thin line between bacterial ‘virulence’ and ‘fitness' or ‘colonization’ factors, and question the definition of enterobacterial virulence factors.

scholarly journals Molecular Epidemiologic Approaches to Urinary Tract Infection Gene Discovery in Uropathogenic Escherichia coli

2000 ◽  
Vol 68 (4) ◽  
pp. 2009-2015 ◽  
Author(s):  
Lixin Zhang ◽  
Betsy Foxman ◽  
Shannon D. Manning ◽  
Patricia Tallman ◽  
Carl F. Marrs
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Dna Sequences ◽  
Bacterial Infections ◽  
Gene Discovery ◽  
Population Characteristics ◽  
E Coli ◽  
K 12

ABSTRACT Urinary tract infection (UTI) is one of the most frequently acquired bacterial infections. The vast majority of UTIs are caused by a large, genetically heterogeneous group of Escherichia coli. This genetic diversity has hampered identification of UTI-related genes. A three-step experimental strategy was used to identify genes potentially involved in E. coli UTI transmission or virulence: epidemiologic pairing of a UTI-specific strain with a fecal control, differential cloning to isolated UTI strain-specific DNA, and epidemiologic screening to identify sequences among isolated DNAs that are associated with UTI. The 37 DNA sequences initially isolated were physically located all over the tester strain genome. Only two hybridized to the total DNA of the sequencedE. coli K-12 strain; eight sequences were present significantly more frequently in UTI isolates than in fecal isolates. Three of the eight sequences matched to genes for multidrug efflux proteins, usher proteins, and pathogenicity island insertion sites, respectively. Using population characteristics to direct gene discovery and evaluation is a productive strategy applicable to any system.

scholarly journals Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays

2003 ◽  
Vol 185 (6) ◽  
pp. 1831-1840 ◽  
Author(s):  
Ulrich Dobrindt ◽  
Franziska Agerer ◽  
Kai Michaelis ◽  
Andreas Janka ◽  
Carmen Buchrieser ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Dna Sequences ◽  
Bacterial Genome ◽  
Distributional Pattern ◽  
Dna Arrays ◽  
E Coli ◽  
Dna Elements ◽  
Presence And Absence ◽  
K 12

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.

Molecular analysis of mutS expression and mutation in natural isolates of pathogenic Escherichia coli

Microbiology ◽  
2003 ◽  
Vol 149 (5) ◽  
pp. 1323-1331 ◽  
Author(s):  
Baoguang Li ◽  
Ho-Ching T. Tsui ◽  
J. Eugene LeClerc ◽  
Manashi Dey ◽  
Malcolm E. Winkler ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Nucleotide Sequence Analysis ◽  
E Coli ◽  
Pathogenic Escherichia Coli ◽  
The Status ◽  
Natural Isolates ◽  
K 12 ◽  
Rnase T2

Deficiencies in the MutS protein disrupt methyl-directed mismatch repair (MMR), generating a mutator phenotype typified by high mutation rates and promiscuous recombination. How such deficiencies might arise in the natural environment was determined by analysing pathogenic strains of Escherichia coli. Quantitative Western immunoblotting showed that the amount of MutS in a wild-type strain of the enterohaemorrhagic pathogen E. coli O157 : H7 decreased about 26-fold in stationary-phase cells as compared with the amount present during exponential-phase growth. The depletion of MutS in O157 : H7 is significantly greater than that observed for a laboratory-attenuated E. coli K-12 strain. In the case of stable mutators, mutS defects in strains identified among natural isolates were analysed, including two E. coli O157 : H7 strains, a diarrhoeagenic E. coli O55 : H7 strain, and a uropathogenic strain from the E. coli reference (ECOR) collection. No MutS could be detected in the four strains by Western immunoblot analyses. RNase T2 protection assays showed that the strains were either deficient in mutS transcripts or produced transcripts truncated at the 3′ end. Nucleotide sequence analysis revealed extensive deletions in the mutS region of three strains, ranging from 7·5 to 17·3 kb relative to E. coli K-12 sequence, while the ECOR mutator contained a premature stop codon in addition to other nucleotide changes in the mutS coding sequence. These results provide insights into the status of the mutS gene and its product in pathogenic strains of E. coli.

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