Morphogenetic core of the bacteriophage T4 head. Structure of the core in polyheads

How Cells Measure Length on Subcellular Scales

Cells are not just amorphous bags of enzymes, but precise and complex machines. With any machine, it is important that the parts be of the right size, yet our understanding of the mechanisms that control size of cellular structures remains at a rudimentary level in most cases. One problem with studying size control is that many cellular organelles have complex 3D structures that make their size hard to measure. Here we focus on linear structures within cells, for which the problem of size control reduces to the problem of length control. We compare and contrast potential mechanisms for length control to understand how cells solve simple geometry problems.

Structural symmetry and protein function

The majority of soluble and membrane-bound proteins in modern cells are symmetrical oligomeric complexes with two or more subunits. The evolutionary selection of symmetrical oligomeric complexes is driven by functional, genetic, and physicochemical needs. Large proteins are selected for specific morphological functions, such as formation of rings, containers, and filaments, and for cooperative functions, such as allosteric regulation and multivalent binding. Large proteins are also more stable against denaturation and have a reduced surface area exposed to solvent when compared with many individual, smaller proteins. Large proteins are constructed as oligomers for reasons of error control in synthesis, coding efficiency, and regulation of assembly. Symmetrical oligomers are favored because of stability and finite control of assembly. Several functions limit symmetry, such as interaction with DNA or membranes, and directional motion. Symmetry is broken or modified in many forms: quasisymmetry, in which identical subunits adopt similar but different conformations; pleomorphism, in which identical subunits form different complexes; pseudosymmetry, in which different molecules form approximately symmetrical complexes; and symmetry mismatch, in which oligomers of different symmetries interact along their respective symmetry axes. Asymmetry is also observed at several levels. Nearly all complexes show local asymmetry at the level of side chain conformation. Several complexes have reciprocating mechanisms in which the complex is asymmetric, but, over time, all subunits cycle through the same set of conformations. Global asymmetry is only rarely observed. Evolution of oligomeric complexes may favor the formation of dimers over complexes with higher cyclic symmetry, through a mechanism of prepositioned pairs of interacting residues. However, examples have been found for all of the crystallographic point groups, demonstrating that functional need can drive the evolution of any symmetry.

Geometry of phage head construction

The process of phage capsid assembly is reviewed, with particular attention to the probable role of curvature in helping to determine head size and shape. Both measures of curvature (mean curvature and Gaussian curvature, explained in Appendix I), should act best when the assembling shell is spherical, which could account for procapsids having this shape. Procapsids are also relatively thick, which should help head size determination by the mean curvature. The accessory role of inner and outer scaffolds in size determination and head nucleation is also reviewed. Nucleation failure generates various malformations, including non-closure, but the most common is the tube or polyhead, where the subunits' inherent curvature is expressed as a constant mean curvature. This induces lattice distortions that only partly understood. An extra tubular section in normal heads leads to the prolate shape, with a more complex and variable geometry. Newly assembled procapsids are both enlarged and toughened by the head transformation. In the procapsid the Gaussian curvature is uniformly distributed. But toughening tends to equalize bond lengths, so all the Gaussian curvature gets concentrated in the vertices, being zero elsewhere. This explains head angularization. Because of this change in Gaussian curvature, the regular subunit packing in the polyhedral head cannot be mapped onto the procapsid. This explains part of the hexon distortions found in this region. The implications of translocase-induced DNA twist, end rotation and the coiling of packaged DNA, are discussed. The symmetry mismatches between the head, connector and tail are discussed in relation to the possible alpha-helical structures of their DNA channels.

On the structure of the scaffolding core of bacteriophage T4

The scaffolding core in bacteriophages is a temporary structure that plays a major role in determining the shape of the protein shell that encapsulates the viral DNA. In the currently accepted structure for the scaffolding core in bacteriophage T4, there is a symmetry mismatch between the protein shell, which has fivefold symmetry, and the scaffolding core, which is believed to consist of six helical chains. The analysis of T4 giant prohead data that was used to determine this structure made an implicit assumption about the manner in which giant proheads flatten during preparation for electron microscopy. Namely, it was assumed that techniques for analysis of Fourier transforms of flattened single-layer cylinders could be applied independently to the shell and the core. This analysis makes the implicit assumption that connections between the core and the shell do not affect the flattening process, and thus are stretched or broken during the flattening process. Reexamination of the experimental data shows that this assumption is likely to be incorrect. A reanalysis shows that the data could be consistent with six, eight, or 10 helical chains, and is a better match for eight or 10 helical chains. Ten helical chains would match the fivefold symmetry of the shell. The 10-helix core model is particularly attractive because it suggests a Vernier mechanism, which is able to explain the process of length determination in giant head mutants of T4. It is possible that the same assumption has been made for structural analysis of other biological systems. If this is the case, any results obtained should also be reexamined.

On the Structure of the Scaffolding Core of Bacteriophage T4 and Its Role in Head Length Determination

The scaffolding core in bacteriophages is a temporary structure that plays a major role in determining the shape of the protein shell that encapsulates the viral DNA. In the currently accepted structure for the scaffolding core in bacteriophage T4, there is a symmetry mismatch between the protein shell, which has fivefold symmetry, and the scaffolding core, which is believed to consist of six helical chains. Alternate structures for the scaffolding core in T4 are investigated. Starting with the hypothesis that the shell and a 10-helix core would have matching symmetry, a Vernier mechanism is proposed that explains the previously unexplained behavior of the length determination process in giant head mutants of T4. Other possible Vernier mechanisms for core structures containing six and eight helices are also explored. Copyright 1998 Academic Press.

Electron microscopic studies on intracellular phage development--history and perspectives

This review is centered on the applications of thin sections to the study of intracellular precursors of bacteriophage heads. Results obtained with other preparation methods are included in so far as they are essential for the comprehension of the biological problems. This type of work was pioneered with phage T4, which contributed much to today's understanding of morphogenesis and form determination. The T4 story is rich in successes, but also in many fallacies. Due to its large size, T4 is obviously prone to preparation artefacts such as emptying, flattening and others. Many of these artefacts were first encountered in T4. Artefacts are mostly found in lysates, however, experience shows that they are not completely absent from thin sections. This can be explained by the fact that permeability changes induced by fixatives occur. The information gained from T4 was profitably used for the study of other phages. They are included in this review as far as electron microscopic studies played a major role in the elucidation of their morphogenetic pathways. Research on phage assembly pathways and form determination is a beautiful illustration for the power of the integrated approach which combines electron microscopy with biochemistry, genetics and biophysics. As a consequence, we did not restrict ourselves to the review of electron microscopic work but tried to integrate pertinent data which contribute to the understanding of the molecular mechanisms acting in determining the form of supramolecular structures.

Mutations that eliminate the requirement for the vertex protein in bacteriophage T4 capsid assembly

The capsid of bacteriophage T4 is composed of two essential structural proteins, gp23, the major constituent of the capsid, and gp24, a less prevalent protein that is located in the pentameric vertices of the capsid. gp24 is required both to stabilize the capsid and to allow it to be further matured. This requirement can be eliminated by bypass-24 (byp24) mutations within g23. We have isolated, cloned and sequenced several new byp24 mutations. These mutations are cold-sensitive in the absence of gp24, and are located in regions of g23 not known to contain any other mutations affecting capsid assembly. The cold-sensitivity of the byp24 mutations can be reduced by further mutations within g23 (trb mutations). Cloning and sequencing of these trb mutations has revealed that they lie in regions of g23 that contain clusters of mutations that cause the production of high levels of petite and giant phage (ptg mutations). Despite the proximity of the trb mutations to the ptg mutations, none of the ptg mutations has a Trb phenotype. The mutation ptE920g, which is also located near one of the ptg clusters, and which produces only petite and wild-type phage, has been shown to confer a Trb but not a Byp24 phenotype. The relevance of these observations to our understanding of capsid assembly is discussed.

Genetic control of capsid length in bacteriophage T4. VII. A model of length regulation based on DNA size

Four models for head length regulation in bacteriophage T4 are described and discussed. Several length mutants in the major capsid protein gene (23) were studied by sucrose gradient analysis, rotating gel analysis of DNA length, and by mixed infection gene dosage experiments with T4 amber mutants in gene 24. The results show that head length variation is quantized and highly specific, in that certain amino acid changes in gp23 results in reproducible and well-defined head length phenotypes. These data are presented as being most consistent with a vernier-type of head length control mechanism.

A proposed structure of bacteriophage T4 gene product 22--a major prohead scaffolding core protein

Gene 22 of bacteriophage T4 encodes a major prohead scaffolding core protein of 269 amino acid residues. From its nucleotide sequence the gene product (gp) 22 has a predicted Mr of 29.9 and a pI of 4.3. The protein is rich in charged residues (glutamic acid and lysine) and contains low amounts of proline and glycine and no cysteine residues. We suggest that gp22 undergoes limited proteolytic processing which eliminates the short C-terminal piece from the molecule during the early steps of prohead assembly. Most amino acid residues of the gp22 polypeptide chain (80%) have an alpha-helical conformation and form seven peculiar alpha-helices. A model suggesting the spatial organization of gp22 is presented. Three long alpha-helices numbered 1 (1A and 1B), 3, and 5 (5A and 5B) are packed in an antiparallel fashion along the major axis of the road-shaped molecule. Two rather short alpha-helices (2 and 4) are located at the distal and proximal ends of the protein molecule, respectively. Helix number 2, which is a proteolytic fragment of gp22 found in mature T4 heads, is packed with helices 1A and 3, similar to a novel element of supersecondary structure, the alpha alpha-corner. Helix number 4 probably interacts with the gp20 connector of the prohead. The implications of the structure of the gp22 molecule for the assembly of the prohead core are discussed.

Quantized viral DNA packaging revealed by rotating gel electrophoresis

Two classes of missense mutations in the bacteriophage T4 gene coding for the major head protein produce phage with different length heads. The pt (petite) mutations produce phage with normal, intermediate, and isometric heads, whereas ptg (petite and giant) mutations also produce greatly elongated (giant) heads. DNA from petite, normal, and giant particles was clearly resolved by discontinuous rotating gel electrophoresis, and several new species of headful length DNA were found. These results confirm the idea that the major stop points for head length regulation are at Q = 13, 17, and 21, and also show that minor stop points exist at Q = 16, 18 and 20. The existence of these well-defined classes of DNA that correlate with capsid structure suggest that a structural relationship between the scaffold protein and the capsid protein determines head length and thus DNA length.

Length and shape variants of the bacteriophage T4 head: mutations in the scaffolding core genes 68 and 22

The shape and size of the bacteriophage T4 head are dependent on genes that determine the scaffolding core and the shell of the prohead. Mutants of the shell proteins affect mainly the head length. Two recently identified genes (genes 67 and 68) and one already known gene (gene 22), whose products are scaffold constituents, have been investigated. Different types of mutants were shown to strongly influence the proportion of aberrantly shaped particles. By model building, these shape variants could be represented as polyhedral bodies derived from icosahedra, through outgrowths along different polyhedral axes. The normal, prolate particle is obtained by elongation along a fivefold axis. The mutations of the three core genes (genes 67, 68, and 22) affect the width mainly by lateral outgrowths of the prolate particle, although small and large isometric particles are also found. Many of the aberrant particles are multitailed, suggesting a correlation between tail attachment sites and shape.

Isolation and reassembly of bacteriophage T4 core proteins

The products of genes 22, 67 and 68, and the internal proteins IPI, IPII and IPIII, as components of the scaffolding core of the bacteriophage T4 prohead, have been isolated and purified by hydroxylapatite column chromatography. Under conditions promoting reassembly in vitro, the proteins associated into elongated particles of practically constant width but variable length that we have called polycores. Preliminary optical diffraction experiments indicate that polycores may have an ordered structure, possibly helical, as has been suggested for the polyhead core. The coassembly of core proteins and the purified shell protein gp23 results in the formation of core-containing polyheads. Occasionally, prolate core-like particles have been observed but their reproducible formation has not been attained. Attempts to investigate the role of the minor prohead component gp20 in core assembly have been made through the cloning of the corresponding gene in an expression vector and subsequent purification of the protein.

Formation of the prohead core of bacteriophage T4 in vivo

Formation of the prohead core of bacteriophage T4 was not dependent on shell assembly. In mutant infections, where the production or assembly of active shell protein was not possible, naked core structures were formed. The particles were generally attached to the bacterial inner membrane and possessed defined prolate dimensions. The intracellular yield varied between 15 and 71% of a corresponding prohead yield and was dependent on the temperature of incubation. The products of genes 21 and 22 were found to be essential for in vivo core formation, whereas those of genes 20, 23, 24, 31, and 40, as well as the internal proteins I to III, were dispensable.

Gene 20 product of bacteriophage T4. II. Its structural organization in prehead and bacteriophage

The location of gene 20 product of bacteriophage T4 in phage and phage percursors has been determined by immunochemical analysis of polyacrylamide gels, immunoturbidimetry and immunoelectron microscopy. The protein is present at the membrane attachment site of the prehead, a head precursor, and is accessible to the antibodies in the solution. It is present at the tail attachment site of the capsid, partially buried in the structure. In complete phage particles it is totally buried in the structure. It is in contact with the major shell proteins, gp23 and gp23*, respectively, in preheads and capsids, as revealed by partial crosslinking experiments. It forms the upper collar of the neck in necked tails. The lower collar is constructed from other gene products. On the basis of these data a structural model of the neck region of the phage has been derived. This model is consistent with a number of events in phage assembly, such as the role of gp20 in head assembly and DNA packaging, prehead detachment from the bacterial membrane and head-tail attachment. The symmetry mismatch known to occur between head and tail has been localized at the gp20-gp23* contact area.

Tubular Heads in Bacteriophages from Lactic Streptococci

Tubular bacteriophage heads were observed in the lysate of two phages from Streptococcus lactis obtained from single plaques without mutagenesis. The frequency of appearance of the tubular heads was 2.5 and 16%.

Genetic studies on capsid-length determination in bacteriophage T4. II. Genetic evidence that specific protein-protein interactions are involved

A bacteriophage T4 mutation (ptg19-80c) located in gene 23, which encodes the major structural protein of the T4 capsid, results in the production of capsids of abnormal length. Mutations outside gene 23 which partially suppress ptg19-80c have been described in the accompanying paper (D. H. Doherty, J. Virol. 43:641-654, 1982). Characterization of these suppressors was extended. A complementation test suggested that the suppressors were in genes 22 and 24. These genes coded for the major component of the morphogenetic core of the capsid precursor and the vertex protein of the capsid, respectively. The suppressor mutations were found to have no obvious phenotype in the absence of ptg19-80c. Suppression was shown to be allele specific: other ptg mutations at different sites in gene 23 were not suppressed by the suppressors of ptg19-80c. These results indicated that specific interactions among the three proteins gp22, gp23, and gp24 may play a role in the regulation of T4 capsid-length determination. Current models for capsid-length determination are considered in the light of these results.

Isolation and characterization of bacteriophage T4 mutant preheads

To determine the function of individual gene products in the assembly and maturation of the T4 prehead, we have isolated and characterized aberrant preheads produced by mutations in three of the T4 head genes. Mutants in gene 21, which codes for the T4 maturation proteases, produce rather stable preheads whose morphology and protein composition are consistent with a wild-type prehead blocked in the maturation cleavages. Mutants in gene 24 produce similar structures which are unstable because they have gaps at all of their icosahedral vertices except the membrane attachment site. In addition, greatly elongated "giant preheads" are produced, suggesting that in the absence of P24 at the vertices, the distal cap of the prehead is unstable, allowing abnormal elongation of broth the prehead core and its shell. Vertex completion by P24 is required to allow the maturation cleavages to occur, and 24- preheads can be matured to capsids in vitro by the addition of P24. Preheads produced by a temperature-sensitive mutant in gene 23 are deficient in core proteins. We show that the shell of these preheads has the expanded lattice characteristic of the mature capsid as well as the binding sites for the proteins hoc and soc, even though none of the maturation cleavage takes place. We also show that 21- preheads composed of wild-type P23 can be expanded in vitro without cleavage.

The structural organization of DNA packaged within the heads of T4 wild-type, isometric and giant bacteriophages

We present electron microscopic and X-ray diffraction evidence concerning the structural organization of condensed DNA within a series of T4 bacteriophage with the following head morphologies: prolate (wild-type), isometric and giant (with greatly increased axial ratio). In all cases, the DNA helix segments are locally parallel and 27 A apart. For the giant particles, we show that the DNA forms a large coil whose axis is perpendicular to the axis of the phage tail. This evidence, combined with previous results from a series of isometric bacteriophages (Earnshaw and Harrison, 1977), leads to a model for the organization of condensed DNA that may apply to most dsDNA-containing bacteriophages.