Complete Genome Sequence of the Enterobacter cancerogenus Bacteriophage Enc34

Abstract

Enterobacter cancerogenus is widely distributed in nature and is generally recovered from environmental or vegetal sources. In some cases, it has also been associated with human infections. In this study, the complete genomic sequence of virulent E. cancerogenus bacteriophage Enc34 was determined. The Enc34 genome is 60,364 bp in length and contains 80 open reading frames. To our knowledge, this is the first report of a bacteriophage infecting E. cancerogenus.

GENOME ANNOUNCEMENT

Bacteriophages are very common organisms in all natural environments. Due to their highly specific host recognition, bacteriophages have potential as therapeutic agents in the treatment of certain human and plant bacterial infections (3, 6) and as useful diagnostic tools (12). Enterobacter cancerogenus (synonym, Enterobacter taylorae) (8) is a facultatively anaerobic Gram-negative bacterium that is generally recovered from environmental or vegetal sources and is considered mostly phytopathogenic (1). It is also a naturally occurring human gut symbiont that is known to exhibit resistance to certain antibiotics, such as aminopenicillins and cephalosporins (13). E. cancerogenus can cause infections of the bones and joints associated with severe trauma or crush injuries (2, 9). Here, we report the full genome sequence and organization of novel virulent bacteriophage Enc34, which infects E. cancerogenus.

Bacteriophage Enc34 was purified from E. cancerogenus lysate by ultracentrifugation in a cesium chloride gradient. Morphologically, bacteriophage Enc34 has an icosahedral head and long, noncontractile tail, which indicate that it belongs to the family Siphoviridae (4). The genomic DNA of Enc34 was isolated by proteinase K treatment and phenol-chloroform extraction. Genome sequencing was performed by primer walking at Microsynth in Switzerland. Putative open reading frames (ORFs) were identified by GeneMark.hmm (10) and GeneMarkS (7) software. The translated ORF products were compared with known protein sequences using BLASTP (5) and the nonredundant public GenBank database. The tRNA sequences were analyzed using the tRNAscan-SE server (11).

The genomic sequence of bacteriophage Enc34 contains 60,364 bp of linear double-stranded DNA with a G+C content of 51.07%. A similarity search for homologous genome sequences found only 42% query coverage (displaying 73 to 79% identity) with Staphylococcus phage SA1 (GenBank accession number, GU169904); however, the SA1 genome comprises 147,303 bp, which is 2.4 times larger than the Enc34 genome. A total of 80 putative ORFs were detected, with the shortest containing 60 amino acids. Seventy-five of the proposed genes had ATG initiation codons, four began with GTG, and one began with TTG. The genes were organized into functional clusters encoding proteins for (i) DNA replication and packaging, (ii) head and tail morphogenesis, (iii) host lysis, and (iv) DNA regulation and modification. No tRNA genes were found. Forty-five of the ORFs were annotated as hypothetical proteins. The DNA replication and packaging module contained genes encoding a DNA primase, DNA polymerase and DNA helicase, as well as small and large terminase subunits and the phage portal protein. Three structural proteins were encoded in the head morphogenesis module, and one of these proteins was predicted to be processed by the prohead protease. As proposed for other bacteriophages with Gram-negative hosts, the lysis module included the holin, endolysin, Rz, and Rz1 proteins arranged in the canonical order.

In conclusion, to our knowledge, this is the first report of a bacteriophage that is lytic for E. cancerogenus. Further experiments will address the detailed study of phage head assembly and lysis mechanisms.

Nucleotide sequence accession number.

The complete genome sequence of bacteriophage Enc34 is available in GenBank under accession number JQ340774.