The Characteristics and Genome Analysis of vB_AviM_AVP, the First Phage Infecting Aerococcus viridans

Abstract

Aerococcus viridans is an opportunistic pathogen that is clinically associated with various human and animal diseases. In this study, the first identified A. viridans phage, vB_AviM_AVP (abbreviated as AVP), was isolated and studied. AVP belongs to the family Myoviridae. AVP harbors a double-stranded DNA genome with a length of 133,806 bp and a G + C content of 34.51%. The genome sequence of AVP showed low similarity (<1% identity) to those of other phages, bacteria, or other organisms in the database. Among 165 predicted open reading frames (ORFs), there were only 69 gene products exhibiting similarity (≤65% identity) to proteins of known functions in the database. In addition, the other 36 gene products did not match any viral or prokaryotic sequences in any publicly available database. On the basis of the putative functions of the ORFs, the genome of AVP was divided into three modules: nucleotide metabolism and replication, structural components, and lysis. A phylogenetic analysis of the terminase large subunits and capsid proteins indicated that AVP represents a novel branch of phages. The observed characteristics of AVP indicate that it represents a new class of phages.

Keywords: Aerococcus viridans; genome analysis; opportunistic pathogen; phage.

Figure 1

The morphology of vB_AviM_AVP (AVP). AVP was negatively stained with 2% phosphotungstic acid (PTA) and examined by transmission electron microscopy (TEM) at an accelerating voltage of 80 kV. The scale bar represents 100 nm.

Figure 2

One-step growth curve for vB_AviM_AVP (AVP) in Aerococcus viridans AV-X1. Shown are samples treated with (▲) and without (●) chloroform at different time points. The values indicate means and standard deviations (SD) (n = 3).

Figure 3

Genetic and physical organization of the vB_AviM_AVP (AVP) genome. The 165 ORFs of AVP are depicted, and the direction of transcription is indicated by arrows. The G + C content and skew of AVP are also shown. The circle map of the AVP genome was made using CGView (http://wishart.biology.ualberta.ca/cgview/) [40].

Figure 4

Graphical representation of the vB_AviM_AVP (AVP) genome. The 165 ORFs are depicted and the direction of transcription is indicated by arrows. Proposed modules are based on hypothetical functions predicted through bioinformatic analysis. The genome map was drawn using CLC Main Workbench, version 7.7.3 (CLC Bio-Qiagen, Aarhus, Denmark).

Figure 5

Phylogenetic tree based on the terminase large subunits (A) and capsid proteins (B) of selected phages. Both the terminase large subunits and capsid proteins were compared using PhyML version 3.0, and the phylogenetic trees were generated using the maximum likelihood method with 100 bootstrap replicates.

Figure 5

Phylogenetic tree based on the terminase large subunits (A) and capsid proteins (B) of selected phages. Both the terminase large subunits and capsid proteins were compared using PhyML version 3.0, and the phylogenetic trees were generated using the maximum likelihood method with 100 bootstrap replicates.