Terminase host factor: a histone-like E. coli protein which can bind to the cos region of bacteriophage lambda DNA

DNA packaging and developmental intermediates of a broad host range Vibrio vulnificus bacteriophage 71A-6

The structural intermediates in the capsid assembly and DNA packaging pathway of Vibrio vulnificus bacteriophage 71A-6, a rod-shaped double-stranded DNA podovirus, were isolated by ultracentrifugation and studied by electron microscopy, SDS-PAGE and pulsed-field gel electrophoretic analysis. Bacteriophage 71A-6 synthesized rod-shaped capsids (mean length=200+/-8 nm; mean width=47+/-3 nm n=50) during its development. Several host proteins that probably help in the assembly and maturation of the capsids were attached to these capsids as spherical structures. A capsid-DNA or DNA packaging complex that consisted of the mature capsids, DNA and a 42.5-kDa protein was also isolated. The size of the capsids increased in length and decreased in width (mean length=220+/-8 nm; mean width=45+/-3 nm n=50) either during or after the DNA packaging. The capsid fractions contained about 12 phage structural proteins and eight host proteins. At least three proteins were tentatively identified: a 38.5-kDa major capsid protein, a 35.2-kDa tail protein and 42.5-kDa packaging initiator or terminator protein. The size of the bacteriophage 71A-6 genome was determined to be 143.0-kb by pulsed-field gel electrophoresis. The total mass of all the mature phage proteins corresponded to only 14.0% of the coding capacity of phage genome.

Integration host factor (IHF) stimulates binding of the gpNu1 subunit of lambda terminase to cos DNA

The lambda terminase enzyme binds to the cohesive end sites (cos) of multimeric replicating lambda DNA and introduces staggered nicks to regenerate the 12 bp single-stranded cohesive ends of the mature phage genome. In vitro this endonucleolytic cleavage requires spermidine, magnesium ions, ATP and a host factor. One of the E. coli proteins which can fulfill this latter requirement is Integration Host Factor (IHF). IHF and the gpNu1 subunit of terminase can bind simultaneously to their own specific binding sites at cos. DNase I footprinting experiments suggest that IHF may promote gpNu1 binding. Although no specific gpNu1 binding to the left side of cos can be detected, this DNA segment does play a specific role since a cos fragment that does not include the left side or whose left side is replaced by non-cos sequences, is unable to bind gpNu1 unless either spermidine or IHF is present. Binding studies on the right side of cos using individual or combinations of gpNu1 binding sites I, II and III indicate that binding at sites I and II is not optimal unless site III is present.

The interaction of E. coli integration host factor and lambda cos DNA: multiple complex formation and protein-induced bending

The interaction of E. coli's integration Host Factor (IHF) with fragments of lambda DNA containing the cos site has been studied by gel-mobility retardation and electron microscopy. The cos fragment used in the mobility assays is 398 bp and spans a region from 48,298 to 194 on the lambda chromosome. Several different complexes of IHF with this fragment can be distinguished by their differential mobility on polyacrylamide gels. Relative band intensities indicate that the formation of a complex between IHF and this DNA fragment has an equilibrium binding constant of the same magnitude as DNA fragments containing lambda's attP site. Gel-mobility retardation and electron microscopy have been employed to show that IHF sharply bends DNA near cos and to map the bending site. The protein-induced bend is near an intrinsic bend due to DNA sequence. The position of the bend suggests that IHF's role in lambda DNA packaging may be the enhancement of terminase binding/cos cutting by manipulating DNA structure.

Mechanism of cos DNA cleavage by bacteriophage lambda terminase: multiple roles of ATP

In the terminus-generating (ter) reaction of phage lambda, the phage enzyme terminase catalyzes the production of staggered nicks within the cohesive-end nicking site (cosN). Although the two nicks are related by a rotational symmetry axis that bisects cosN, the in vitro ter reaction is strikingly asymmetric at the nucleotide level. Nicking of the lambda r strand precedes nicking of the I strand. Furthermore, when the two nicking reactions are uncoupled, they have different nucleotide cofactor requirements. ATP plays critical roles during cos cleavage: First, nicking of both DNA strands is stimulated by the addition of ATP. Second, ATP is required for the correct specificity of r-strand nicking since, in the absence of nucleotide, the r-strand nick is shifted 8 bases to the left. Studies with nonhydrolyzable analogs indicate that ATP hydrolysis is not required for these functions. However, after the two nicks are made, terminase catalyzes a disengagement of the cohered ends in a reaction that requires ATP hydrolysis.