The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80
Bacteriophage EC1-UPM is an N4-like bacteriophage which specifically infects Escherichia coli O78:K80, an avian pathogenic strain that causes colibacillosis in poultry. The complete genome sequence of bacteriophage EC1-UPM was analysed and compared with other closely related N4-like phage groups t...
| Main Authors: | , , , , |
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| Format: | Article |
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BioMed Central
2013
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| _version_ | 1796971629409992704 |
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| author | Gan, Han Ming Sieo, Chin Chin Gee, Shirley Hoon Tang Omar, Abdul Rahman Ho, Yin Wan |
| author_facet | Gan, Han Ming Sieo, Chin Chin Gee, Shirley Hoon Tang Omar, Abdul Rahman Ho, Yin Wan |
| author_sort | Gan, Han Ming |
| collection | UPM |
| description | Bacteriophage EC1-UPM is an N4-like bacteriophage which specifically infects Escherichia coli O78:K80,
an avian pathogenic strain that causes colibacillosis in poultry. The complete genome sequence of bacteriophage
EC1-UPM was analysed and compared with other closely related N4-like phage groups to assess their genetic
similarities and differences.Bacteriophage EC1-UPM displays a very similar codon usage profile with its host and does not contain any tRNA gene. Comparative genomics analysis reveals close resemblance of bacteriophage EC1-UPM to three N4-like bacteriophages namely vB_EcoP_G7C, IME11 and KBNP21 with a total of 44 protein coding genes shared at 70% identity threshold. The genomic region coding for the tail fiber protein was found to be unique in bacteriophage EC1-UPM. Further annotation of the tail fiber protein using HHpred, a highly sensitive homology detection tool, reveals the presence of protein structure homologous to various polysaccharide processing proteins in its Cterminus. Leveraging on the availability of multiple N4-like bacteriophage genome sequences, the core genes of N4-like bacteriophages were identified and used to perform a multilocus phylogenetic analysis which enabled the construction of a phylogenetic tree with higher confidence than phylogenetic trees based on single genes. We report for the first time the complete genome sequence of a N4-like bacteriophage which is lytic
against avian pathogenic Escherichia coli O78:K80. A novel 928 amino acid residues tail fiber protein was identified in EC1-UPM which may be useful to further the understanding of phage-host specificity. Multilocus phylogenetic analysis using core genes of sequenced N4-like phages showed that the evolutionary relationship correlated well with the pattern of host specificity. |
| first_indexed | 2024-03-06T08:15:50Z |
| format | Article |
| id | upm.eprints-29880 |
| institution | Universiti Putra Malaysia |
| last_indexed | 2024-03-06T08:15:50Z |
| publishDate | 2013 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | upm.eprints-298802016-01-20T02:29:52Z http://psasir.upm.edu.my/id/eprint/29880/ The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 Gan, Han Ming Sieo, Chin Chin Gee, Shirley Hoon Tang Omar, Abdul Rahman Ho, Yin Wan Bacteriophage EC1-UPM is an N4-like bacteriophage which specifically infects Escherichia coli O78:K80, an avian pathogenic strain that causes colibacillosis in poultry. The complete genome sequence of bacteriophage EC1-UPM was analysed and compared with other closely related N4-like phage groups to assess their genetic similarities and differences.Bacteriophage EC1-UPM displays a very similar codon usage profile with its host and does not contain any tRNA gene. Comparative genomics analysis reveals close resemblance of bacteriophage EC1-UPM to three N4-like bacteriophages namely vB_EcoP_G7C, IME11 and KBNP21 with a total of 44 protein coding genes shared at 70% identity threshold. The genomic region coding for the tail fiber protein was found to be unique in bacteriophage EC1-UPM. Further annotation of the tail fiber protein using HHpred, a highly sensitive homology detection tool, reveals the presence of protein structure homologous to various polysaccharide processing proteins in its Cterminus. Leveraging on the availability of multiple N4-like bacteriophage genome sequences, the core genes of N4-like bacteriophages were identified and used to perform a multilocus phylogenetic analysis which enabled the construction of a phylogenetic tree with higher confidence than phylogenetic trees based on single genes. We report for the first time the complete genome sequence of a N4-like bacteriophage which is lytic against avian pathogenic Escherichia coli O78:K80. A novel 928 amino acid residues tail fiber protein was identified in EC1-UPM which may be useful to further the understanding of phage-host specificity. Multilocus phylogenetic analysis using core genes of sequenced N4-like phages showed that the evolutionary relationship correlated well with the pattern of host specificity. BioMed Central 2013 Article PeerReviewed Gan, Han Ming and Sieo, Chin Chin and Gee, Shirley Hoon Tang and Omar, Abdul Rahman and Ho, Yin Wan (2013) The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80. Virology Journal, 10. art. no. 308. pp. 1-8. ISSN 1743-422X http://virologyj.biomedcentral.com/articles/10.1186/1743-422X-10-308 |
| spellingShingle | Gan, Han Ming Sieo, Chin Chin Gee, Shirley Hoon Tang Omar, Abdul Rahman Ho, Yin Wan The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 |
| title | The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 |
| title_full | The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 |
| title_fullStr | The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 |
| title_full_unstemmed | The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 |
| title_short | The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 |
| title_sort | complete genome sequence of ec1 upm a novel n4 like bacteriophage that infects escherichia coli o78 k80 |
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