Full-genome sequence of a novel myovirus, GF-2, infecting Edwardsiella tarda: comparison with other Edwardsiella myoviral genomes

Abstract

Edwardsiellosis, which is caused by Edwardsiella tarda, a Gram-negative bacterium, is one of the most serious infectious diseases in both marine and freshwater fish farms worldwide. Previously, we reported the complete genome sequences of three E. tarda-lytic bacteriophages (two podoviruses and a myovirus), which were isolated from fish tissues and fish-rearing seawater. Further genomic information regarding E. tarda phages is important for understanding phage-host interactions as well as for applications of the phages for the control of disease. Here, we report the complete genome sequence of a novel E. tarda phage (GF-2) of myovirus morphology (family Myoviridae), isolated from tissue homogenates of a cultured Japanese flounder (Paralichthys olivaceus) that succumbed to edwardsiellosis in Japan. The size of the entire genome was 43,129 bp, with a GC content of 51.3 % and containing 82 open reading frames (ORFs). The GF-2 genome possesses lysogeny-related genes that have not been found in the reported Edwardsiella phage genomes. Comparative genomics of Edwardsiella myophages suggest that the C-terminal domains of the tail fiber proteins have relevance to their host specificity. Thus, GF-2 genome information provides a novel resource for our understanding of the molecular mechanisms involved in their host specificity and for detection of E. tarda in aquaculture environments.

Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages

“…The five exceptional newly sequenced phages, IME-EC2 ( Escherichia ; Accession No. KF591601; Hua et al , 2014), Ss1 ( Cronobacter ; KM058087; Endersen et al , 2014), CVT22 (Citrobacter; KP774835; Tikhe et al , 2015), SEN34 ( Salmonella , KT630649), and GF-2 ( Edwardsiella ; AP014629; Yasuike et al , 2015) are founding phages of three new lytic and two new temperate clusters (our unpublished observations). The small number of new clusters generated by the many recently sequenced genomes supports the notion that, at least for the best-studied genera of this bacterial family, Escherichia and Salmonella, most of the common tailed phage types that infect them have been discovered.…”

Characterization of a Highly Virulent Edwardsiella anguillarum Strain Isolated From Greek Aquaculture, and a Spontaneously Induced Prophage Therein

“…Measurements made on the obtained TEM pictures, revealed that the Edno5 bacteriophage has an icosahedral (isometric) capsid of 68.1 ± 3.5 nm equipped with a long rigid tail of 74.5 ± 4.1 × 18.2 ± 2.3 nm ( n = 14). Endo5 virions resemble those of the E. tarda myoviruses GF-2 and MSW-3 since they were about 61 and 60 nm in capsid diameter and 81.6 and 80 nm in tail length, respectively (Kawato and Nakai, 2012; Yasuike et al, 2015).…”

“…Edwardsiella is also a member of Enterobacteriaceae family, thus comparing these already studied systems to E. anguillarum- Edno5 phage system, reveals potentially conserved regulatory mechanisms. Specifically, gene homologs of cI , cro , and cII that are present in bacteriophage lambda are also found in the genome of Edno5 and relative E. tarda phage GF-2 (Yasuike et al, 2015). The lysogenic pathway can be interrupted by the expression of the cro gene (gene 53 in Edno5) which turns off early gene transcription during the lytic cycle.…”

“…We showed that the strain belonged to the newly described species E. anguillarum (Shao et al, 2015) and was closely related to the E. piscicida -like strain isolated from diseased groupers in the Red Sea (Ucko et al, 2016). Furthermore, the isolate contained a spontaneously inducible intact prophage that is genetically similar to both a prophage found in the bacterial genome of an E. piscicida -like strain EA181011 (Reichley et al, 2015) and the free bacteriophage GF-2 (Yasuike et al, 2015) that has been isolated against E. tarda .…”

Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe

“…The sequence of the GF-2 phage was present in 90% (27/30) of the total genomes analyzed and in all of the European genomes. Historically, Yasuike et al described for the first time the GF-2 phage, a myovirus lytic bacteriophage in 2015 [22]. It was isolated from a cultured Japanese flounder that succumbed to Edwardsiella tarda , a Gram-negative Enterobacteriaceae that is the most serious pathogen in both marine and freshwater fish farms worldwide.…”