# A Novel Benthic Phage Infecting _Shewanella_ with Strong Replication Ability
## 3 Results and Discussion
### Genomic Features of the Phage S0112
\begin{table}
\begin{tabular}{c c c c c c c c} \hline \hline _Shewanella_ & **Host Strains** & **Family** & **Size (Kb)** & **GC\%** & **Protein** & **No. of** & & \\
**Phages\({}^{\text{a}}\)** & & & & & & & & **tRNAs** & **Isolation Source** \\ \hline S0112 & _Shewanella indica_ & _Siphevitate_ & 62.286 & 44.7 & 102 & 0 & Coastal sediment \\ Sp001 & _S. putfications_ & _Siphevitate_ & 54.789 & 49.4 & 67 & 0 & Sewage \\
3/49 & _S. [PERSON]_ & _Siphevitate_ & 40.161 & 42 & 70 & 0 & Baltic Sea ice \\
1/44 & _S. [PERSON]_ & _Siphevitate_ & 49.64 & 39.8 & 75 & 0 & Baltic Sea ice \\ SppY2U05 & _S. putfications_ & _Siphevitate_ & 54.319 & 50.63 & 65 & 0 & Waste effluents \\
1/41 & _S. [PERSON]_ & _Moyevitate_ & 43.51 & 42.7 & 69 & 0 & Baltic Sea ice \\ SFC11 & _S. [PERSON]_ & _Moyevitate_ & 42.279 & 59.1 & 40 & 0 & Seawater \\ SppY2U01 & _S. [PERSON]_ & _Moyevitate_ & 43.567 & 55.72 & 49 & 0 & Waste effluents \\
1/44 & _S. Trigiliararia_ & _Moyevitate_ & 133.824 & 36.9 & 235 & 3 & Baltic Sea ice \\
1/40 & _S. [PERSON]_ & _Moyevitate_ & 139.004 & 36.9 & 236 & 3 & Baltic Sea ice \\ \hline \hline \end{tabular}  
\end{table} 
Table 3: The genome information of ten _Shewanella_ phages. The structure/morphogenesis module includes head-tail connector protein (S0112_066), major capsid protein (S0112_071 and _076), tail completion protein (S0112_074), tail terminator protein (S0112_075), tail chaperonin (S0112_078), tail length tape measure protein (S0112_079), virion structural protein (S0112_081), tail assembly structural protein (S0112_082, _084, _085_, and _086), minor tail protein (S0112_083 and _087), peptidase C39 family protein (S0112_034), _alpha/beta_ hydrolase (S0112_060), and putative endolysin (S0112_062). Among this module, the tape measure protein usually exists in siphoviruses and is involved in the assembly of phage tails and the determination of the tail length [44]. Endolysin is a lytic enzyme used to lyse the cell wall of the host. The endolysin consists of two domains: One is the N-terminal domain, which is responsible for degrading bacterial peptidoglycan, and the other is the C-terminal domain, called holin, which is mainly bound to the cell membrane [45]. The DNA replication/recombination/metabolism module in phage genome includes ten ORFs, whose gene products include DNA polymerase I (S0112_092), DNA polymerase subunit B (S0112_093), DNA/RNA helicase (S0112_005), primase/helicase (S0112_018), DNA-binding domain protein (S0112_017), exonuclease (S0112_006), endonuclease (S0112_036), ATPase (S0112_009), P-loop containing nucleoside triphosphate hydrolase (S0112_011), and DprA-like protein (S0112_023). Among them, DNA polymerase is vital for phage DNA replication, and its coding gene is relatively conservative in many tailed phages [46]. Primase and helicase found in the genome of phage S0112 are of key importance for DNA replication. The primosome formed by primase and helicase can synthesize a short RNA primer, which can be elongated by DNA polymerase [47]. Exonucleases are enzymes that participate in the process of breaking phosphodiester bonds at either 3' or 5' end [48]. Other enzymes including endonuclease, DNA-binging protein, and DprA-like protein play important roles in DNA repair and transcription regulation. It is worth noting that ATPase encoded by ORF  
Figure 6: Genomic map of phage S0112. The phage S0112 genome is presented schematically with ORFs indicated by leftward or rightward oriented arrows, based on the direction of transcription. Gene features (DNA packaging, structure/morphogenesis protein, DNA replication/recombination/metabolism, and queuosine biosynthesis) are color-coded according to the legend below the figure. 9 is similar to the ATPase of the benthic _Vibrio_ phage VpKK5, which was also isolated from coastal sediments. ATPase is important for DNA replication, DNA recombination, and DNA packaging [18]. Interestingly, we found ORF 99 in the phage genome of S0112 is an auxiliary metabolic gene encoding the MazG nucleotide pyrophosphhydrolase domain [49].