Identification and characterization of spontaneous deletions within the Sp11-Sp12 prophage region of Escherichia coli O157:H7 Sakai

Chun Chen, Carrie R. Lewis, Kakolie Goswami, Elisabeth L. Roberts, Chitrita Debroy, Edward G. Dudley

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Prophages make up 12% of the enterohemorrhagic Escherichia coli genome and play prominent roles in the evolution and virulence of this food-borne pathogen. Acquisition and loss of and rearrangements within prophage regions are the primary causes of differences in pulsed-field gel electrophoresis (PFGE) patterns among strains of E. coli O157:H7. Sp11 and Sp12 are two tandemly integrated and putatively defective prophages carried by E. coli O157:H7 strain Sakai. In this study, we identified 3 classes of deletions that occur within the Sp11-Sp12 region, at a frequency of ca. 7.74x10-4. One deletion resulted in a precise excision of Sp11, and the other two spanned the junction of Sp11 and Sp12. All deletions resulted in shifts in the XbaI fragment pattern observed by PFGE. We sequenced the inducible prophage pool of Sakai but did not identify any mature phage particles corresponding to either Sp11 or Sp12. Deletions containing pchB and psrC, which are Sp11-carried genes encoding proteins known or suspected to regulate type III secretion, did not affect the secretion levels of the EspA or EspB effector. Alignment of the Sp11- Sp12 DNA sequence with its corresponding regions in other E. coli O157:H7 and O55:H7 strains suggested that homologous recombination rather than integrase-mediated excision is the mechanism behind these deletions. Therefore, this study provides a mechanism behind the previously observed genetic instability of this genomic region of E. coli O157:H7.

Original languageEnglish (US)
Pages (from-to)1934-1941
Number of pages8
JournalApplied and environmental microbiology
Volume79
Issue number6
DOIs
StatePublished - Mar 1 2013

Fingerprint

Prophages
Escherichia coli O157
Pulsed Field Gel Electrophoresis
pulsed-field gel electrophoresis
secretion
electrokinesis
gel
Enterohemorrhagic Escherichia coli
Integrases
enterohemorrhagic Escherichia coli
Genomic Instability
Homologous Recombination
homologous recombination
food pathogens
virulence
bacteriophages
Bacteriophages
recombination
Virulence
genomics

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

Cite this

Chen, Chun ; Lewis, Carrie R. ; Goswami, Kakolie ; Roberts, Elisabeth L. ; Debroy, Chitrita ; Dudley, Edward G. / Identification and characterization of spontaneous deletions within the Sp11-Sp12 prophage region of Escherichia coli O157:H7 Sakai. In: Applied and environmental microbiology. 2013 ; Vol. 79, No. 6. pp. 1934-1941.
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abstract = "Prophages make up 12{\%} of the enterohemorrhagic Escherichia coli genome and play prominent roles in the evolution and virulence of this food-borne pathogen. Acquisition and loss of and rearrangements within prophage regions are the primary causes of differences in pulsed-field gel electrophoresis (PFGE) patterns among strains of E. coli O157:H7. Sp11 and Sp12 are two tandemly integrated and putatively defective prophages carried by E. coli O157:H7 strain Sakai. In this study, we identified 3 classes of deletions that occur within the Sp11-Sp12 region, at a frequency of ca. 7.74x10-4. One deletion resulted in a precise excision of Sp11, and the other two spanned the junction of Sp11 and Sp12. All deletions resulted in shifts in the XbaI fragment pattern observed by PFGE. We sequenced the inducible prophage pool of Sakai but did not identify any mature phage particles corresponding to either Sp11 or Sp12. Deletions containing pchB and psrC, which are Sp11-carried genes encoding proteins known or suspected to regulate type III secretion, did not affect the secretion levels of the EspA or EspB effector. Alignment of the Sp11- Sp12 DNA sequence with its corresponding regions in other E. coli O157:H7 and O55:H7 strains suggested that homologous recombination rather than integrase-mediated excision is the mechanism behind these deletions. Therefore, this study provides a mechanism behind the previously observed genetic instability of this genomic region of E. coli O157:H7.",
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Identification and characterization of spontaneous deletions within the Sp11-Sp12 prophage region of Escherichia coli O157:H7 Sakai. / Chen, Chun; Lewis, Carrie R.; Goswami, Kakolie; Roberts, Elisabeth L.; Debroy, Chitrita; Dudley, Edward G.

In: Applied and environmental microbiology, Vol. 79, No. 6, 01.03.2013, p. 1934-1941.

Research output: Contribution to journalArticle

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T1 - Identification and characterization of spontaneous deletions within the Sp11-Sp12 prophage region of Escherichia coli O157:H7 Sakai

AU - Chen, Chun

AU - Lewis, Carrie R.

AU - Goswami, Kakolie

AU - Roberts, Elisabeth L.

AU - Debroy, Chitrita

AU - Dudley, Edward G.

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AB - Prophages make up 12% of the enterohemorrhagic Escherichia coli genome and play prominent roles in the evolution and virulence of this food-borne pathogen. Acquisition and loss of and rearrangements within prophage regions are the primary causes of differences in pulsed-field gel electrophoresis (PFGE) patterns among strains of E. coli O157:H7. Sp11 and Sp12 are two tandemly integrated and putatively defective prophages carried by E. coli O157:H7 strain Sakai. In this study, we identified 3 classes of deletions that occur within the Sp11-Sp12 region, at a frequency of ca. 7.74x10-4. One deletion resulted in a precise excision of Sp11, and the other two spanned the junction of Sp11 and Sp12. All deletions resulted in shifts in the XbaI fragment pattern observed by PFGE. We sequenced the inducible prophage pool of Sakai but did not identify any mature phage particles corresponding to either Sp11 or Sp12. Deletions containing pchB and psrC, which are Sp11-carried genes encoding proteins known or suspected to regulate type III secretion, did not affect the secretion levels of the EspA or EspB effector. Alignment of the Sp11- Sp12 DNA sequence with its corresponding regions in other E. coli O157:H7 and O55:H7 strains suggested that homologous recombination rather than integrase-mediated excision is the mechanism behind these deletions. Therefore, this study provides a mechanism behind the previously observed genetic instability of this genomic region of E. coli O157:H7.

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DO - 10.1128/AEM.03682-12

M3 - Article

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SN - 0099-2240

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