The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands
Background: Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd+) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothio...
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| Format: | Article |
| Language: | English |
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BioMed Central
2015
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| Online Access: | http://eprints.um.edu.my/13369/1/12864_2015_Article_1421.pdf |
| _version_ | 1796946559675400192 |
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| author | Ho, W.S. |
| author_facet | Ho, W.S. |
| author_sort | Ho, W.S. |
| collection | UM |
| description | Background: Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to
in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd+)
is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the
modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to
detect the presence of the dnd operon in Dnd+ E. coli strains and to improve their typeability. Investigations into
the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is
harboured in various diverse genomic islands.
Results: The dndBCDE genes (dnd operon) were detected in all Dnd+ E. coli strains by PCR. The addition of thiourea
improved the typeability of Dnd+ E. coli strains to 100% using PFGE and the Dnd+ phenotype can be observed in
both clonal and genetically diverse E. coli strains.
Genomic analysis of 101 dnd operons from genome sequences of Enterobacteriaceae revealed that the dnd operons
of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of dnd
operons of 52 E. coli genomes together with their respective immediate genetic environments revealed a total
of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated
dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and the genomic context of the 7 islands
(with 1 representative genome from each type of genetic organization) were also highly variable, suggesting
multiple recombination events. This is also the first report where two dnd operons were found within a strain
although the biological implication is unknown. Surprisingly, dnd operons were frequently found in pathogenic E.
coli although their link with virulence has not been explored.
Conclusion: Genomic islands likely play an important role in facilitating the horizontal gene transfer of the dnd
operons in E. coli with 7 different types of islands discovered so far.
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| first_indexed | 2024-03-06T05:33:37Z |
| format | Article |
| id | um.eprints-13369 |
| institution | Universiti Malaya |
| language | English |
| last_indexed | 2024-03-06T05:33:37Z |
| publishDate | 2015 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | um.eprints-133692015-04-22T03:19:49Z http://eprints.um.edu.my/13369/ The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands Ho, W.S. QR Microbiology Background: Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd+) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the dnd operon in Dnd+ E. coli strains and to improve their typeability. Investigations into the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is harboured in various diverse genomic islands. Results: The dndBCDE genes (dnd operon) were detected in all Dnd+ E. coli strains by PCR. The addition of thiourea improved the typeability of Dnd+ E. coli strains to 100% using PFGE and the Dnd+ phenotype can be observed in both clonal and genetically diverse E. coli strains. Genomic analysis of 101 dnd operons from genome sequences of Enterobacteriaceae revealed that the dnd operons of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of dnd operons of 52 E. coli genomes together with their respective immediate genetic environments revealed a total of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and the genomic context of the 7 islands (with 1 representative genome from each type of genetic organization) were also highly variable, suggesting multiple recombination events. This is also the first report where two dnd operons were found within a strain although the biological implication is unknown. Surprisingly, dnd operons were frequently found in pathogenic E. coli although their link with virulence has not been explored. Conclusion: Genomic islands likely play an important role in facilitating the horizontal gene transfer of the dnd operons in E. coli with 7 different types of islands discovered so far. BioMed Central 2015 Article PeerReviewed application/pdf en http://eprints.um.edu.my/13369/1/12864_2015_Article_1421.pdf Ho, W.S. (2015) The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands. BMC Genomics, 16 (199). |
| spellingShingle | QR Microbiology Ho, W.S. The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands |
| title | The dnd operon for DNA phosphorothioation
modification system in Escherichia coli is located
in diverse genomic islands
|
| title_full | The dnd operon for DNA phosphorothioation
modification system in Escherichia coli is located
in diverse genomic islands
|
| title_fullStr | The dnd operon for DNA phosphorothioation
modification system in Escherichia coli is located
in diverse genomic islands
|
| title_full_unstemmed | The dnd operon for DNA phosphorothioation
modification system in Escherichia coli is located
in diverse genomic islands
|
| title_short | The dnd operon for DNA phosphorothioation
modification system in Escherichia coli is located
in diverse genomic islands
|
| title_sort | dnd operon for dna phosphorothioation modification system in escherichia coli is located in diverse genomic islands |
| topic | QR Microbiology |
| url | http://eprints.um.edu.my/13369/1/12864_2015_Article_1421.pdf |
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