Condensed Genome Structure

Abstract

Large, tailed dsDNA-containing bacteriophage genomes are packaged to a conserved and high density (~500 mg/ml), generally in ~2.5-nm, duplex-to-duplex, spaced, organized DNA shells within icosahedral capsids. Phages with these condensate properties, however, differ markedly in their inner capsid structures: (1) those with a naked condensed DNA, (2) those with many dispersed unstructured proteins embedded within the DNA, (3) those with a small number of localized proteins, and (4) those with a reduced or DNA-free internal protein structure of substantial volume. The DNA is translocated and condensed by a high-force ATPase motor into a procapsid already containing the proteins that are to be ejected together with the DNA into the infected host. The condensed genome structure of a single-phage type is unlikely to be precisely determined and can change without loss of function to fit an altered capsid size or internal structure. Although no such single-phage condensed genome structure is known exactly, it is known that a single general structure is unlikely to apply to all such phages.

Molecular architecture of tailed double-stranded DNA phages

“…The proteins can be dispersed within the capsid interior or form ordered structures which occupy a substantial fraction of the capsid volume. 104 Some of these proteins ("pilot proteins") are injected into the host cell during infection prior or along with the phage DNA. For example, phage T4 capsid contains ~40 copies of the gpalt protein (75 kDa), which are probably located near or on the portal protein.…”

“…For example, phage T4 capsid contains ~40 copies of the gpalt protein (75 kDa), which are probably located near or on the portal protein. 13,104 Gpalt is an ADP-ribosyltransferase which modifies the host's RNA polymerase resulting in preferential recognition of phage early promoters.…”

“…106 In addition, T4 capsid contains more than 1000 molecules of 3 small internal proteins (8-20 kDa), which are dispersed within the DNA. 13,104 One of these proteins (IPI) helps to protect the phage genome from degradation by the host's endonucleases. 107,108 Capsids of T7-like phages contain internal cores assembled on the portal protein.…”

Visualization of uncorrelated, tandem symmetry mismatches in the internal genome packaging apparatus of bacteriophage T7

“…Functions of the layers include DNA binding/loading (small terminase), ATPase hydrolysis (large terminase), DNA channel (portal), and DNA condensation (internal proteins, sometimes in several layers). The detailed structural basis and functional mechanism of the DNA packaging process are under extensive investigation (4)(5)(6).…”

“…Inside some bacteriophages, which include T7 (19,21,22), P-SSP7 (11), and e15 (17), a roughly cylindrical, multilayered structure (that we will call the core stack) is attached to the portal ring. Diverse functions have been suggested for the core stack in capsid assembly, DNA packaging, and DNA ejection (4,19,23). Molecular-dynamics simulations have shown that the T7 core stack has a significant effect on packaged DNA conformation via excluded volume (24).…”