Table 1.
Summary of the gene content of functional modules present in the S. aureus phages.
| Groups | Family | Phage Morphogenesis | Host Cell Lysis | DNA Metabolism | DNA Packaging | Lysogeny | Virulence | Antimicrobial Resitance | Represent Phage |
|---|---|---|---|---|---|---|---|---|---|
| Lineage I | Podoviridae | major head protein (1), upper collar protein (1), lower collar protein (1), minor structural protein (1), and tail fibers (2) | lysin (2) and holin (1) | DNA polymerase (1) and DNA binding protein (1) | DNA packaging protein (1) | - | - | - | SapYZU11 (MW864250) |
| Clade IIa | Herelleviridae | major capsid protein (2), capsid protein (1), portal protein (2), tail protein (2), microtubule-associated protein (1), tail sheath protein (1), and baseplate J-like protein (1) | lysin (5) and holin (1) | DNA synthesis (3), DNA polymerase I (2), DNA repair recombinase (1), DNA-binding protein (1), RNA polymerase (1), DNA helicase (1), Type III restriction enzyme (1), DNA methylase (1), DNA repair exonuclease (1) and DNA primase (1) | DNA packaging protein (1) | transposase (5) | virulence-associated E family protein (1) | - | SapYZU15 (MW864252) |
| Clade IIb | Herelleviridae | portal protein (1), major capsid protein (1), major tail sheath (1), tail tape measure protein (1), baseplate J-like protein (1), and major tail protein (2) | lysin (5) and holin (1) | Type III restriction enzyme (1), DNA helicase (1), DNA primase/helicase (1), DNA synthesis (2), DNA polymerase I (2) and DNA modification protein (1) | DNA packaging protein (2) | recombinase (1) | dUTP pyrophosphatase (2) and virulence-associated E family protein (1) | beta-lactamase (1) | phiSA_BS2 (MH028956.1) |
| Clade IIc | Herelleviridae | head protein (1), portal protein (1), prohead protease (1), major capsid protein (1), tail sheath protein (1), tail morphogenetic protein (8), and Baseplate J-like protein (1) | lysin (2) and holin (1) | RNA ligase (1), Type III restriction enzyme (1), DNA helicase (1), DNA primase (1), DNA synthesis (2), DNA polymerase (2), RNA polymerase (1) and DNA sliding clump inhibitor (1) | DNA packaging protein (1) | recombinase (2) | - | - | 676Z (JX080302.2) |
| Clade IIIa | Siphoviridae | portal protein (1), major capsid protein (1), head-tail connector protein (1), tail protein (3), and tail tape measure protein (2) | lysin (1) and holin (1) | DNA polymerase (1) | DNA packaging protein (2) | Clp protease (1) and repressor (1) | gamma-hemolysin (1), PVL (1), dUTP pyrophosphatase (1) and virulence-associated E family protein (1) | - | 3A (NC_007053.1) |
| Clade IIIb | Siphoviridae | minor structural protein (1), tail protein (2), tape measure protein (1), major tail protein (1), head-tail adaptor protein (2), major capsid protein (1), and portal protein (1) | lysin (2) and holin (1) | DNA-binding protein (1) and DNA polymerase III (1) | DNA packaging protein (1) | integrase (1), anti-repressor protein (1) and Clp protease (1) | dUTP pyrophosphatase (1), PVL (1), complement inhibitor SCIN-A (1) and staphylokinase (1) | - | 23MRA (NC_028775.1) |
| Clade IIIc | Siphoviridae | minor structural protein (1), tail length tape measure protein (1), tape measure protein (1), major tail protein (1), capsid protein (1), prohead protease (1), and portal protein (1) | lysin (2) and holin (1) | DNA-binding protein (1) and DNA repair protein (1) | DNA packaging protein (3) | anti-repressor protein (1), repressor (1) and integrase (1) | beta-hemolysin (2), staphylokinase (1), and dUTP pyrophosphatase (1) | beta-lactamase (1) | 3_AJ_2017 (KX232515.1) |
| Clade IIId | Siphoviridae | portal protein (1), minor capsid protein (1), head protein (1), head-tail connector protein (1), tail protein (3), tail assembly chaperone (1), minor structural protein (1), and baseplate upper protein (1) | lysin (2) and holin (1) | DNA-binding protein (1) and DNA helicase (1) | DNA packaging protein (2) | integrase (1), excisionase (1), Repressor (1) and anti-repressor (1) | dUTP pyrophosphatase (1) | - | 11 (NC_004615.1) |
| Clade IIIe | Siphoviridae | portal protein (1), minor head protein (1), scaffolding protein (1), head-tail connector protein (1), head closure protein (1), tail protein (2), and baseplate upper protein (1) | lysin (2) and holin (1) | DNA-binding protein (1) and DNA helicase (1) | DNA packaging protein (3) | integrase (1) and anti-repressor protein (1) | dUTP pyrophosphatase (1) | - | 29 (NC_007061.1) |
| Lineage II singleton | Herelleviridae | portal protein (1), prohead protease (1), major capsid protein (1), tail sheath protein (1), tail tube protein (1), tail tape measure protein (1), baseplate J-like protein (1), and tail morphogenetic protein (1) | lysin (2) and holin (1) | RNA polymerase (1), Type III restriction enzyme (1), DNA helicase (1), DNA primase (1), DNA synthesis (3), DNA polymerase I (1) and DNA-binding protein (1) | DNA packaging protein (2) | recombination exonuclease (2) and transposase (1) | virulence-associated E family protein (1) | - | Twort (NC_007021.1) |
| Lineage II singleton | Siphoviridae | portal protein (1), head-tail adaptor protein (1), major capsid protein (1), major tail protein (1) and tail length tape measure protein (1) | lysin (2) and holin (1) | RNA ligase (1), DNA-binding protein (1), DNA primase (1), DNA helicase (1), DNA synthesis (2) and DNA polymerase (1) | DNA packaging protein (4) | integrase (1) | - | - | VB_SauS_SA2 (MH356730.1) |
| Lineage II singleton | Siphoviridae | tail fiber protein (3), tail tape measure protein, major tail protein (4), capsid protein (1), prohead protease (1), and portal protein (1) | lysin (1) and holin (1) | DNA-binding protein (1) and DNA helicase (1) | DNA packaging protein (3) | - | dUTP pyrophosphatase (1) | - | vB_SauS_IMEP5 (KX156762.1) |
| Lineage III singleton | Siphoviridae | portal protein (1), capsid protein (1), tail protein (2), tape measure protein (1), and minor structural protein (1) | lysin (1) | DNA polymerase (1) | DNA packaging protein (1) | integrase (1) and Clp protease (1) | dUTP pyrophosphatase (1) and virulence-associated E family protein (1) | 2638A (NC_007051.1) | |
| Lineage III singleton | Siphoviridae | portal protein (1), head morphogenesis protein (1), scaffolding protein (1), major head protein (1), head-tail connector protein (1), head closure protein (1), major tail protein (1), tail protein (2), and baseplate upper protein (2) | lysin (2) and holin (1) | DNA-binding protein (2) and DNA helicase (1) | DNA packaging protein (2) | integrase (1) | dUTP pyrophosphatase (1) | - | EW (NC_007056.1) |
| Lineage III singleton | Siphoviridae | portal protein (1), capsid protein (1), head-tail connector protein (1), tail tube protein (1), tail protein (1), tail tape measure protein (1), tail fiber protein (2), and minor structural protein (1) | lysin (1) and holin (1) | DNA-binding protein (1) and DNA helicase (1) | DNA packaging protein (2) | integrase (1) | PVL (1), dUTP pyrophosphatase (1) and virulence-associated protein E family protein (2) | - | vB_SauS_fPfSau02 (MK348510.1) |
| Lineage III singleton | Siphoviridae | portal protein (1), minor capsid protein (1), capsid and scaffold protein (1), capsid protein (1), tail protein (4), head-tail connector protein (1), major tail protein (1), tail assembly chaperone (1), and baseplate upper protein (1) | lysin (2) and holin (1) | DNA-binding protein (1) | DNA packaging protein (2) | integrase (1) and anti-repressor (1) | PVL (2) and dUTP pyrophosphatase (1) | - | 187 (NC_007047.1) |