Packaging of DNA into bacteriophage heads: A model

A model is suggested for the geometry of DNA entry into a bacteriophage head. It accounts for recent observations indicating absence of a unique, ordered sequence of windings in the packaged DNA.     

Double-stranded DNA organization in bacteriophage heads: an alternative toroid-based model.

Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent will all available data. Recently we proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here we propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure.     

Mode of DNA packing within bacteriophage heads

Electron micrographs of five different DNA bacteriophages, as prepared by drying in thin films of negative stain, frequently show their heads to be disrupted and flattened. In such cases DNA strands, no larger than 2.5 nm in diameter, become visible, either contained within partially ruptured capsids or completely ejected from severely ruptured ones. Seen in either aspect, the strands appear with circular outline; in some cases a set of concentric circles (or a tightly wound spiral) is evident.Two alternative models of DNA packing within phage heads are proposed. Both are consistent with the electron microscopic observations and, as applied specifically to T4 phage heads, they are also consistent with available data from birefringence studies. One model proposes that the DNA, in simple double-helix form, is wound into a ball. The other suggests that the DNA is wound like a spool, with a greater number of turns in the central region than at the two ends and with the spool axis perpendicular to the axis of the phage particle. The available evidence does not permit a choice to be made between the two models.     

Model for DNA packaging into bacteriophage T4 heads.

The mechanism of DNA packaging into bacteriophage T4 heads in vivo was investigated by glucosylation of hydroxymethylcytosine residues in a conditionally glucose-deficient host. Cytoplasmic DNA associated with partially packaged ts49 heads can be fully glucosylated, whereas DNA already packaged into these heads is shown to be resistant to glucosylation. After temperature shift and completion of arrested packaging into the reversible temperature-sensitive ts49 head, the structure of the DNA in the mature ts49 phage was investigated by restriction enzyme digestion, autoradiography, and other techniques. Such mature DNA appears to be fully glucosylated along part of its length and nonglucosylated on the remainder. Its structure suggests that the DNA is run into the head linearly and unidirectionally from one mature end and that there is little sequence specificity in that portion of the T4 DNA which first enters the capsid. This technique should be useful in investigation of the three-dimensional structure of first- and last-packaged DNA within the head; preliminary studies including autoradiography of osmotically shocked phage suggest that the DNA which first enters the head is deposited toward the center of the capsid and that the end of the DNA which first enters the head exits first upon injection. In conjunction with studies of the structure of condensed DNA, the positions and functions of T4 capsid proteins in DNA packaging, and the order of T4 packaging functions [Earnshaw and Harrison, Nature (London) 268:598-602, 1977; Hsiao and Black, Proc. Natl. Acad. Sci. U.S.A. 74:3652-3656, 1977; Müller-Salamin et al., J. Virol. 24:121-134, 1977; Richards et al., J. Mol. Biol. 78:255-259, 1973], the features described above suggest the following model: the first DNA end is fixed to the proximal apex of the head at p20 and the DNA is then pumped into the head enzymatically by proteins (p20 + p17) which induce torsion in the DNA molecule.     

Packaging of DNA in bacteriophage heads: some considerations on energetics

We have made quantitative estimates of some of the energetic factors to be considered in packaging of double-stranded DNA in virus particles. Numerical calculations were made using parameters appropriate for T4 bacteriophage. The unfavorable factors, and the Gibbs free energies per mole virus at 20°C associated with them, are bending, 1.5 × 10³ kcal/mol; conformational restriction upon condensation, 5.1 × 10² kcal/mol; polyelectrolyte repulsion, 2.1 × 10⁵kcal/mol; and melting or kinking, 6.9 × 10³ kcal/mol. These must be counterbalanced in the assembled phage by noncovalent bonding interactions between protein subunits in the phage-head shell; by interactions between the DNA and polyvalent cations, especially putrescine and spermidine; nad perhaps by repulsive excluded volume and electrostatic interaction between the DNA and acidic polypeptides. Indeed, a rough estimate of the standard free energey of interaction between T4 DNA and the putrescine and spermidine contained in the head is --2.1 × 10⁵ kcal/mol. In the absence of the other two sources of stabilization, each head protein subunit must contribute about 210 kcal/mol of binding energy.     

Structural aberrations in T-even bacteriophage. VI. Molecular weight of DNA from giant heads

Cummings et al. (1973) reported that whenl-canavanine was chased from a T-even. bacteriophage-infected culture with its analog,l-arginine, a new type of aberrant particle was formed. These particles, which were termed “lollipops”, had giant heads as long as 44 normal head lengths, and were filled with DNA. We have now separated these particles into different size classes ranging from about three to 13 normal head lengths and measured the molecular weight of their DNA. The DNA released from intact phage particles by neutral or alkaline detergent lysis was characterized using a recently described biophysical technique which determines DNA molecular weight from solution viscoelasticity. The maximum DNA size correlated roughly with phage head length, indicating that these giant heads were often filled with single, long DNA molecules rather than with several normal-sized molecules. Many of the heads, however, must have contained several molecules, since a large amount of DNA of less than maximum size was present. In alkali the native molecules separated into single strands of approximately the same length as that of the native molecules.     

Studies of DNA packaging into the heads of bacteriophage lambda

During the assembly of bacteriophage λ heads, a head-like, DNA-free structure called petite λ, is first constructed. Into this, λ DNA is then packaged. In this paper we examine early interactions between λ DNA and petite λ in a cell-free system. The two major findings of this paper are: (1) when seen through the electron microscope, an early petite λ-λ DNA complex appears with the circular petite λ having the DNA crossing through its center. These resemble a bead on a string or the Greek letter φ (hence they are called φ structures). The λ A protein is required in the formation of φ structures. Also, φ structures can be found in bacteria infected with phage λ. (2) The polyamine putrescine is required for phage head assembly. An earlier reported requirement for spermidine can be replaced by the addition of putrescine. Polyamine is required in the DNA packaging reaction after the packaging has begun.     

Processing of bacteriophage lambda DNA during its assembly into heads

DNA purified from bacteriophage λ added to a cell-free extract derived from induced λ lysogens can be packaged into infectious phage particles (Kaiser & Masuda, 1973). In this paper the structure of the DNA which is the substrate for in vitro packaging and head assembly is described. The active precursor is a multichromosomal polymer that contains covalently closed cohesive end sites. Neither circular or linear DNA monomers nor polymers with unsealed cohesive ends are packaged efficiently into heads. The unit length monomer is packaged when it is either contained in the interior of a polymer (both of its ends are in cos sites) or when it has a free left end and a cos site on its right. The monomer unit with a free right end is not a substrate for packaging.A procedure is given for the purification of λ DNA fragments that contain either the left or the right cohesive end. The fragments are produced by digesting λ DNA with the site-specific Escherichia coli R₁ endonuclease; the left and right ends are separated by sedimentation through a sucrose gradient. These fragments are used to construct small polymers that have a unit length λ monomer with (1) a free left end and a closed right end, (2) a free right end and a closed left end, or (3) both ends closed in cos sites.     

Maturation of the head of bacteriophage T4. III. DNA packaging into preformed heads

An estimate was made of the amount of DNA packaged into gene 49-defective heads when P49 is activated by a temperature shift. The uptake of DNA into preformed heads following activation of P49 was studied using bromo-deoxyuridine as a label. The rate of inactivation by visible light of the phage matured in the presence of BrdU as well as their buoyant density in CsCl, indicate that over half of the particles package, on the average, at least 25% of the DNA complement following P49 activation. This is a minimum estimate, since the BrdU-labeled DNA has to compete with unlabeled DNA. Analysis on alkaline sucrose gradients of the size of the DNA extracted from phage matured in the presence of BrdU following irradiation reveals that extended irradiation at 313 nm breaks the DNA close to half of its original size. These experiments clearly show that up to half of the DNA can be packaged into the preformed heads made at high temperature following activation of the product of gene 49 (P49), strongly supporting the pathway for phage head maturation described by Laemmli &; Favre (1973).The so-called τ-particles, which accumulate in 24-defective cells, can serve as precursors of the mature phage (Bijlenga et al., 1973). We have measured the uptake of BrdU-labeled DNA into τ-particles during their maturation. We find that a very large proportion of DNA made after activation of P24 is apparently incorporated into preformed τ-particles as these particles are converted into mature heads. This indicates that the τ-particles contain very little or no DNA prior to P24 activation and supports the pathway described by Laemmli &; Favre (1973).     

Cloning of mini-mu bacteriophage in cosmids: in vivo packaging into phage lambda heads

A technique has been developed that permits the packaging of mini-Mu-carrying cosmids into phage lambda heads. This procedure has several advantages over packaging into Mu helper capsids: the amounts of DNA to be packaged can be increased, the packaging efficiency is improved, and the stability of transducing lysates is high.     

Interrelationships between polyamines and nucleic acids

Summary The distribution of radioactivity from ³H-putrescine was studied in intact and degenerated sciatic nerves, and spinal ganglia of rats by means of high resolution autoradiography. During the first three days after the administration of the labeled putrescine, the main proportion of radioactive material in the nerves was represented by spermidine and putrescine. Both, in intact and degenerating nerves, developed silver grains were deposited in all cellular components of the nervous tissue, the myelin sheath being markedly tagged. Perineural tissue was also labeled considerably, however, there was no significant amount of label in the extracellular space and in the collagen fibrils. The possible physiological significance of putrescine and spermidine in myelin and in other cellular components of nerves is discussed.Herrn Prof. Dr. W. Krücke zum 60. Geburtstag gewidmet.     

Relationship between polyamines and macromolecules in germinating yeast ascospores.

The accumulation of spermidine and/or spermine was not necessary for normal macromolecule biosynthesis or germination and outgrowth of Saccharomyces cerevisiae spores.     

Joining of bacteriophage T4D heads and tails: A kinetic study by inelastic light scattering

We have used inelastic laser light scattering to study the kinetics of the spontaneous assembly of heads and tails of bacteriophage T4D to form noninfectious tail fiberless particles. For interpretation of the kinetics, it was first necessary to determine the physical properties of the strongly scattering phage parts. For heads, these are D_{20,w = 3.60 × 10⁻⁸cm²/s, 820,w = 1025 S, M = 1.76 × 10⁸}. For tail fiberless particles, D_20,w = 3.14 × 10⁻⁸cm²/s, 8_20,w = 968 S, and M = 1.95 × 10⁸. The kinetics of the head-tail joining process was followed by measuring the time variation of the homodyne scattering autocorrelation function. This was interpreted as a sum of exponentials whose decay constants were known from the scattering angle and the diffusion coefficients, and whose amplitudes were related to the concentrations of reactants and products. Scattering experiments at 22 °C gave a bimolecular rate constant of 1.02 × 10⁷m⁻¹ s⁻¹, while infectivity assays at 30 °C gave a rate constant of 1.28 × 10⁷. Adjustment of both rate constants to 20 °C, assuming diffusion controlled reaction, gave 0.97 × 10⁷ and 0.98 × 10⁷m⁻¹ s⁻¹, respectively. This rate is about $\text{1}\text{500}$ that predicted by Smoluchowski theory for a diffusion controlled reaction between two spherical particles; the discrepancy is largely explicable from orientational factors.     

Assembly of the head of bacteriophage P22: X-ray diffraction from heads,proheads and related structures

We have used electron microscopy and small-angle X-ray diffraction to study the three principal structures found in the head assembly pathway of Salmonella phage P22. These structures are, in order of their appearance in the pathway: proheads, unstable filled heads (which lose their DNA and become empty heads upon isolation), and phage. In addition, we can convert proheads to an empty head-like form (the empty prohead) in vitro by treating them with 0.8% sodium dodecyl sulfate at room temperature.We have shown that proheads are composed of a shell of coat protein with a radius of 256 Å, containing within it a thick shell or a solid ball (outer radius 215 Å) of a second protein, the scaffolding protein, which does not appear in phage. The three other structures studied are all about 10% larger than proheads, having outer shells with radii of about 285 Å. Empty heads and empty proheads appear identical by small-angle X-ray diffraction to a resolution of 25 Å, both being shells about 40 Å thick. Phage appear to be made up of a protein shell identical to that in empty heads and empty proheads, within which is packed the DNA.Some details of the DNA packing are also revealed by the diffraction pattern of phage. The inter-helix distance is about 28 Å, and the hydration is about 1.5 g of water per g of DNA. Certain aspects of the pattern suggest that the DNA interacts in a specific mariner with the coat protein subunits on the inside edge of the protein shell.Thus, the prohead-to-head transformation involves, in addition to the loss of an internal scaffold and its replacement by DNA, a structural transition in the outer shell. Diffraction from features of the surface organization in these structures indicates that the clustering of the coat protein does not change radically during the expansion. The fact that the expansion occurs in vitro during the formation of empty proheads shows that it is due to the bonding properties of the coat protein alone, although it could be triggered in vivo by DNA -protein interactions. The significance of the structural transition is discussed in terms of its possible role in the control of head assembly and DNA packaging.     

Functional antagonism between c-Jun and MyoD proteins: a direct physical association.

The product of the proto-oncogene Jun inhibits myogenesis. Constitutive expression of Jun in myoblasts interferes with the expression and the function of MyoD protein. In transient transfection assays Jun inhibits transactivation of the MyoD promoter, the muscle creatine kinase enhancer, and a reporter gene linked to MyoD DNA-binding sites. Conversely, MyoD suppresses the transactivation by Jun of genes linked to an AP-1 site. We demonstrate that both in vivo and in vitro MyoD and Jun proteins physically interact. Mutational analysis suggests that this interaction occurs via the leucine zipper domain of Jun and the helix-loop-helix region of MyoD.