Abstract
N4-like bacteriophages are a class of virulent Podoviridae phages for which few genome sequences are present in GenBank. IME11, a novel lytic Escherichia bacteriophage with a wide host range, was isolated, and the whole genome was sequenced. It has a circular double-stranded DNA genome of 72,570 bp. Genomic analysis showed that it resembles another Escherichia phage, vB_EcoP_G7C. Here we announce its complete genome and major findings from its annotation.
GENOME ANNOUNCEMENT
Escherichia coli is a Gram-negative bacterium that acts as an opportunistic pathogen. It forms biofilms (9) which give rise to infections in diarrhea patients (6) and sepsis patients (2). An increasing incidence of multidrug-resistant E. coli strains has been reported (8). Bacteriophages have been used to control multidrug-resistant E. coli strains (4). We isolated IME11 from the sewage of the no. 307 hospital in Beijing, China. The phage infected 13 of all 31 enteropathogenic E. coli strains from the clinical laboratory of the no. 307 hospital, which implies that it has potential as an agent against enteropathogenic E. coli.
N4-like bacteriophages are a class of virulent Podoviridae phages, for which few genome sequences are present in GenBank. They include Escherichia phage N4 (11), Enterobacter phage EcP1 (GenBank ID: HQ641380), Escherichia phage vB_EcoP_G7C (7), Erwinia phage vB_EamP-S6 (3), Pseudomonas phages LIT1 and LUZ7 (5), Silicibacter phage DSS3φ2, and Sulfitobacter phage EE36ϕ1 (12). IME11 is a new member of the N4-like viruses.
Genomic DNA was extracted from the phage stock by the proteinase K/SDS method (10). Whole-genome sequencing of this organism was performed with the FLX Titanium genome sequencer system (350× coverage), and the raw sequences were assembled using the Roche 454 Newbler 2.5 assembler. The prediction of open reading frames (ORFs) was performed using the RAST annotation server (1) and Kodon (Applied Maths, Sint-Martens-Latem, Belgium).
The complete genome of phage IME11 revealed a length of 72,570 bp with a G+C content of 43.1%. Of the 91 ORFs identified, 18 were annotated as known functional genes. Structural proteins included major coat protein, phage neck whiskers, anchor domain protein, and phage tape measure protein, while nonstructural proteins included DNA primase, DNA helicase, phage integrase, single-stranded DNA-binding protein, DNA polymerase I, RNA polymerase, and dCTP deaminase. The remaining 73 gene products were annotated as hypothetical proteins, probably due to insufficient database information about the functional genes of N4-like phage genomes. Genomic analysis showed that this phage resembles the Escherichia phage vB_EcoP_G7C. The complete genome of this phage provides new insights and information regarding the phage's genetic characteristics and its interactions with Escherichia coli.
Nucleotide sequence accession number.
The complete genome sequence of bacteriophage IME11 was submitted to GenBank under the accession number JX880034.
ACKNOWLEDGMENTS
This research was supported by a grant from the National Natural Science Foundation of China (no. 81072350), China Mega-Project on Major Drug Development (no. 2011ZX09401-023), China Mega-Project on Infectious Disease Prevention (no. 2011ZX10004-001), and State Key Laboratory of Pathogen and Biosecurity Program (no. SKLPBS1113).
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