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The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80

Gan, Han Ming, Sieo, Chin Chin, Tang, Shirley Gee Hoon, 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, vol. 10, pp. 1-8, doi: 10.1186/1743-422X-10-308.

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Title The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80
Formatted title The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80
Author(s) Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Sieo, Chin Chin
Tang, Shirley Gee Hoon
Omar, Abdul Rahman
Ho, Yin Wan
Journal name Virology journal
Volume number 10
Article ID 308
Start page 1
End page 8
Total pages 8
Publisher BioMed Central
Place of publication London, Eng.
Publication date 2013-10-18
ISSN 1743-422X
Keyword(s) Animals
Birds
Cluster Analysis
Coliphages
DNA, Viral
Escherichia coli
Genome, Viral
Molecular Sequence Data
Phylogeny
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Viral Proteins
bacteriophage EC1-UPM
tail fiber protein
complete genome
multilocus phylogenetic analysis
Summary BACKGROUND: 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.

RESULTS: 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 C-terminus. 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.

CONCLUSION: 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.
Language eng
DOI 10.1186/1743-422X-10-308
Field of Research 1108 Medical Microbiology
0605 Microbiology
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2013, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30098062

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.