TABLE X.
Protein–protein interactions of phage ϕ29 including phage–host interactionsa
| ϕ29 1 | Function 1 | ϕ29 2 | Function 2 | References |
|---|---|---|---|---|
| gp2 | DNA polymerase | gp3 | DNA terminal protein TP | Kamtekar et al., 2006; Blanco et al., 1987; Dufour et al., 2000; González-Huici et al., 2000 |
| gp3 | DNA terminal protein TP | gp1 | Membrane-associated early protein | Bravo et al., 2000 |
| gp3 | DNA terminal protein TP | gp3 | DNA terminal protein TP | Serna-Rico et al., 2003 |
| gp3 | DNA terminal protein | gp16 | Packaging ATPase | Guo et al., 1987 Grimes and Anderson, 1997 |
| gp4 | Late gene activator | gp4 | Late gene activator | Badia et al., 2006 Mencía et al., 1996b |
| gp4 | Late gene activator | gp6 | Histone-like, nonspecific DNA-binding protein | Calles et al., 2002; Camacho and Salas, 2001 |
| gp6 | Histone-like, nonspecific dsDNA-binding protein | gp6 | Histone-like, nonspecific dsDNA-binding protein | Abril et al., 1999; Pastrana et al., 1985 |
| gp7 | Scaffolding protein | gp7 | Scaffolding protein | Morais et al., 2003 |
| gp7 | Scaffolding protein | gp8 | Major head protein | Lee and Guo, 1995 |
| gp7 | Scaffolding protein | gp10 | Upper collar/connector protein | Guo et al., 1991; Lee and Guo, 1995 |
| gp10 | Upper collar/connector protein | gp10 | Upper collar/connector protein | Guasch et al., 2002; Simpson et al., 2001 |
| gp12 | Preneck appendage protein (anti-receptor) | gp12 | Preneck appendage protein (anti-receptor) | Xiang et al., 2009 |
| gp13 | Tail-associated, peptidoglycan-degrading enzyme | gp9 | Tail knob protein | García et al., 1983 |
| gp13 | Tail-associated, peptidoglycan-degrading enzyme | gp13 | Tail-associated, peptidoglycan-degrading enzyme | Xiang et al., 2008 |
| gp16.7 | Replication organizer; DNA-binding membrane protein p16.7 | gp16.7 | Replication organizer; DNA-binding membrane protein p16.7 | Asensio et al., 2005; Albert et al., 2005; Crucitti et al., 1998; Serna-Rico et al., 2003; Meijer et al., 2001b |
| gp16.7 | Replication organizer; DNA-binding membrane protein p16.7 | gp3 | DNA terminal protein TP | Serna-Rico et al., 2003 |
| gp17 | Early protein involved in early DNA replication | gp6 | Histone-like, nonspecific dsDNA-binding protein | Crucitti et al. 2003 |
| gp17 | Early protein involved in early DNA replication | gp17 | Early protein involved in early DNA replication | Crucitti et al., 2003 |
| gp56 = gp0.8 | Host uracil-DNA glycosylase inhibitor | gp56= gp0.8 | Host uracil-DNA glycosylase inhibitor | Serrano-Heras et al., 2007) |
| ϕ29–Bacillus subtilis interactions | ||||
| gp4 | Late gene activator (3) | RpoA | RNA polymerase subunit α | Mencía et al., 1996a; Monsalve et al., 1996b |
| gp16.7 | Replication organizer, DNA-binding membrane protein gp16.7 (2) | MreB | Actin-like cytoskeleton protein | Muñoz-Espín et al., 2009 |
| gp56 = gp0.8 | UDG inhibitor (1) | UDG | Uracil-DNA glycosylase | Serrano-Heras et al., 2006 |
a
Data from BOND, IntACT, and PDB (ϕ29, Taxon id 186846). All proteins are termed “gp” (gene product), although they are also termed “p” (protein), e.g., gp4 = p4. In the phage–host interaction list, the first protein is from ϕ29, the second from B. subtilis. (1) Host RNAP binds via α subunit to p4 (i) bound at the late promoter PA3, thus activating late transcription and (ii) bound to the promoter PA2c, thus blocking transcription through promoter clearance inhibition. (2) PPI plays a role in the organization of ϕ29 DNA replication as peripheral helix-like structures. (3) Inhibition of host UDG; avoids removal of uracil from ϕ29 DNA via UDG-base excision repair.