Complete Genome Sequence of Bacteriophage phiAC-1 Infecting Acinetobacter soli Strain KZ-1

Abstract

To date, a number of bacteriophages (phages) infecting Acinetobacter species have been reported and characterized. However, Acinetobacter phages which infect A. soli have not been investigated yet. Here, we report the complete genome sequence of Acinetobacter phage phiAC-1, which belongs to the Myoviridae, infecting Acinetobacter soli strain KZ-1.

GENOME ANNOUNCEMENT

Members of the genus Acinetobacter are ubiquitously distributed in natural environments (3, 6) and have been shown to have high levels of intrinsic antibiotic resistance (1, 2). To date, several phages infecting Acinetobacter species have been reported, and most of them were known to infect A. baumannii (4, 7, 12) or A. johnsonii (11). However, phages infecting a potential human pathogen (10), A. soli, have not yet been reported.

Acinetobacter phage phiAC-1 (BP-4001) and its host strain (Acinetobacter sp.) were purchased from the Bacteriophage Bank at Hankuk University of Foreign Studies in the Republic of Korea. The host bacterial strain was classified as Acinetobacter soli based on its 16S rRNA (GenBank accession no. JX499235) and rpoB (GenBank accession no. JN379292) sequences in our laboratory and finally designated A. soli strain KZ-1. The phage was extremely host specific and did not lyse the other 21 species of Acinetobacter strains, including A. soli KCTC 22184. Morphologically, the phage was classified as a member of the Myoviridae, with an icosahedral head (approximately 40 nm in diameter) and contractile tail (approximately 90 nm in length).

Genomic DNA was extracted as described previously (13), sequenced using the Ion Torrent PGM 314 chip (Life Technologies) at GenoTech Corp. in Korea (approximately 1,028× coverage) and assembled with the CLC Genomics Workbench (CLC bio). The gaps were filled by PCR, and the full-length genome was obtained by sequence assembly using SeqMan II sequence analysis software (DNASTAR). The putative open reading frames (ORFs) were predicted using Glimmer 3.02 (5) and GeneMark.hmm (9), and the putative functions and presences of Pfam domains of the ORFs were analyzed by BLASTP and the HMMER 3.0 program HMMscan (http://hmmer.org/). Putative tRNA genes were searched using tRNAscan-SE (v. 1.21) (8).

The circular, double-stranded DNA genome of phiAC-1 was 43,216 bp in length with a G+C composition of 38.5%, and no tRNA was detected from it. A total of 82 ORFs containing more than 35 amino acid residues were identified, and the total length and capacity of all ORFs were 91.4% (39,492 bp) and 91.0% (39,346 bp), respectively. Based on the genome size and its sequence similarity, the closest relatives of phiAC-1 (≥40.0%) were identified as Acinetobacter phages AB1 (7) and AP22 (12), and 42 out of 50 phage-related ORFs were homologs of these 2 phages, with amino acid identity ranging from 37.1 to 96.4%. Additionally, 8 out of 28 bacteria-related proteins scattered throughout the phiAC-1 genome were similar to proteins from other Acinetobacter species, and 4 ORFs showed no homology to known sequences in the GenBank database.

The putative functions of 21 phage-related ORFs in phiAC-1 were assigned, and they were mainly related to viral morphogenesis and lytic properties. orf71 was predicted as endolysin (similar to chitinase_glyco_hydro_19 [PF00182.14]), whereas no holin or holin-like protein was detected from the BLASTP search. Further studies will be needed to investigate the function of orf71 and the lytic mechanisms of Acinetobacter phage phiAC-1.

Nucleotide sequence accession number.

The complete genome sequence of Acinetobacter phage phiAC-1 was deposited in GenBank under the accession number JX560521.