Subsystem: Phage head and packaging

This subsystem's description is:

Phage head and packaging subsystem designed by Mya, curated by Li, Mel and Ryan.

This subsystem contains proteins of Caudovirales only, those of Microviridae, Leviviridae, Cystoviridae, Inoviridae are not included.


Proteins involved in head formation and structure: procapsid/capsid, vertex, scaffolding/assembly/protease, decoration, maturation and internal core proteins.

Proteins involved in phage packaging: capsid/procapsid/prohead proteins, portals, terminases, scaffolding proteins

For more information, please check out the description and the additional notes tabs, below

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Phage head and packaging subsystem designed by Mya, curated by Li, Mel and Ryan.

This subsystem contains proteins of Caudovirales only, those of Microviridae, Leviviridae, Cystoviridae, Inoviridae are not included.


Proteins involved in head formation and structure: procapsid/capsid, vertex, scaffolding/assembly/protease, decoration, maturation and internal core proteins.

Proteins involved in phage packaging: capsid/procapsid/prohead proteins, portals, terminases, scaffolding proteins
PHAGE HEAD FORMATION

Proteins involved in phage packaging include --
* Major capsid proteins: Proteins that make up the capsid shell of the phage, pentons & hexons. These also lay the groundwork for the formation of the prohead.
* Vertex proteins: Responsible for forming the pentameric vertices of the capsid shell.
* Decoration proteins: decorator proteins stabilize the capsid shell upon rearrangement and placement of capsid proteins that make up the capsid shell. These include HOCs and SOCs, these play a role in enhancing stability of the mature phage head.
* Completion proteins: Carries out the completion of filled heads by making the newly packaged DNA in filled heads resistant to DNase. The protein is assumed to bind to DNA-filled capsids.
* Chaperone proteins: Protein that aids in the folding and assemply of head proteins and their vertices.
* Maturation protease proteins: Responsible for removal of the N-terminal residues in order to convert proteins into other proteins during phage maturation
* Internal (core) proteins: internal (core) protein's play a role in formation of the phage prohead.
* Vertex Proteins: Protein responsible for forming vertices, occasionally these proteins are replaced by portal proteins
* WAC (whisker antigen control) proteins: Whisker proteins that are required for efficient tail fiber attachment during phage assembly


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PHAGE PACKAGING

Virus genomes of dsDNA phages are packaged into their capsid head through a fast and rapid, ATP-powered "machine" (Rao and Feiss, 2008).

Proteins involved in phage packaging include --
* Portal proteins: dodecamer ring of subunits that serves as central channel for DNA to pass through; required for proper DNA packaging.
* Prohead proteins: the assembly of the prohead (the precursor capsid shell) requires the portal protein (where prohead assembly is initiated), the major capsid protein, and scaffold proteins. Prohead assembly is initiated on the portal protein, which are required for proper DNA packaging.
* Scaffolding proteins: assist in assembly, but not in final virion
* Terminases: DNA packaging enzymes with (i) ATPase activity that moves DNA into the prohead through the portal, and (ii) endonucleases that cut concatemeric DNA into single genome units during packaging (though not all contain this second function). Terminases are hetero-oligomers of small DNA recognition subunit, large unit containing the ATPase, the endonuclease, and a motif to recognize and dock to the portal

Tailed dsDNA phages share a common strategy for DNA packaging (summarized below from Rao and Feiss, 2008); see illustrations for a scheme:

1. An empty icosahedron (20 triangular faces and 12 corners) shell, the prohead, is formed from many copies of the major capsid protein

2. At one of the prohead's 12 vertices, a dodecamer portal protein ring localizes in the prohead, with a central channel for DNA passage, and a protrusion outwards of the head, on which the “translocation motor” assembles.

3. DNA packaging is initiated when the small terminase subunit binds specifically to phage concatemeric DNA, typically near DNA cut sites (ie, cos, pac). The terminase binds the DNA and docks on the prohead portal.

4. The dsDNA then enters the prohead through the portal protein ring due to ATP hydrolysis-driven conformational changes of the portal or terminase (Rao and Feiss, 2008).

5. A second cut by the terminase cuts the concatemeric DNA into genome units. In phages with “headful” packaging, terminase makes the terminal cut when the prohead is full, leading to an evolutionary coupling of capsid size and genome length (DNA translocated is often 1.02-1.1 times the unit length of the genome). Other phages (lambda, P2), terminase cuts at specific sites, typically the cos site.

6. The terminase, still bound to the concatemer dsDNA, undocks from the portal and moves on to the next prohead for the next packaging.

7. As the DNA enters the prohead, each major capsid subunit undergoes conformational change into a mature shell, often increasing its capacity 50-100% (note: in T4, expansion and filling activity can be uncoupled). Upon filling, the internal forces are estimated at 50 pN (for phi29), thus head stabilization proteins (gpD in lambda, Soc in T4) are needed to prevent burst (Fuller et al., 2007).

The large terminase translocation ATPase subunit contains a classic DNA binding fold, similar to monomeric helicases (Rao and Feiss, 2008). These terminase large subunits can be classified by their specific enzymatic end-generating function, which determines the type of DNA "ends" they create. This distinction can be recognized in their amino acid sequences, as similar functional types cluster in large terminase amino acid sequence alignment-based trees (Casjens 2005; Duhaime et al., 2010; Sullivan et al., 2009).

LARGE TERMINASE FUNCTIONAL TYPES (Casjens 2005) --
Phage terminase, large subunit (lambda-like 5'-extended COS ends): cos serves as a DNA packaging recognition site, and is where the terminase introduces staggered nicks to regenerate cohesive ends for later cyclization of linear dsDNA post-infection.
* Phage terminase, large subunit (P2-like 5'-extended COS ends): same as lambda-like cos recognition-based
* Phage terminase, large subunit (3'-extended COS ends): same as lambda-like cos recognition-based
* Phage terminase, large subunit (T4-like headful) **classification here also depends on the phage's membership in the T4-core subsystem: terminase binds to pac recognition site and cuts the concatemer, captures a prohead, and translocates the linear dsDNA into the prohead.
* Phage terminase, large subunit (P22-like headful): same as T4-like headful packaging, except initial cuts are not at pac sites
* Phage terminase, large subunit (Mu-like headful):
* Phage terminase, large subunit (GTA headful):
Phage terminase, large subunit (T7-like direct terminal repeats):

phi29-like phages have unique packaging. Along with adenoviruses, they never generate a concatemeric string, but rather replicate as monomers with terminal proteins (gp3) initiating replication, followed by packaging by a strand displacement mechanism (Guo 1987; Rodríguez et al., 2004). Their gp3 is functionally analogous to terminase small subunits, while gp16 analogous to large subunits. Their prohead contains a small packaging RNA (pRNA) required to join gp16 to the portal.

Intriguingly, terminase, portal, and shell proteins of tailed bacteriophages and herpesviruses share conserved features (Rao and Feiss, 2008).