Bacteriophage SPO1 structure and morphogenesis. III. SPO1 proteins and synthesis.

The virion proteins of SPO1 have been determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis methods on purified phage components and on phage lysates. The phage head contains 16 proteins, and the connector or neck structure has an additional 3 proteins not found in the head. The proximal part of the tail, composed of sheath, tube and connecting components, contains six proteins. The distal baseplate is the most complex structure, with 28 proteins identifiable on sodium dodecyl sulfate gels. The maximum number of proteins found in phage subassemblies is 53, which would account for nearly half the coding capacity of the SPO1 genome.     

Mechanism of length determination in bacteriophage lambda tails

The mechanism of length determination in bacteriophage λ tails is discussed as a model for regulation in protein assembly systems.The λ tail is a long flexible tube ending in a conical part and a single tail fiber. Its length is exactly determined in the sense that the number of major tail protein (gpV) molecules, which comprise more than 80% of the mass of the tail, is exactly the same in all tails. Assembly of gpV is regulated by the initiator complex, which contains the tail fiber and the conical part,and by the terminator protein gpU. There are two key points in the assembly of gpV with respect to length determination. (1) Assembly of gpV on the initiator pauses at the correct tail length. Binding of gpU to the tail only fixes the pause firmly. (2) When the tail length is too short, binding of gpU to tails is inhibited.Deletions and a duplication (both in frame) in gene H, which codes for one of the proteins in the initiator, result in production of phage particles with altered tail length. Moreover, the tail length is roughly proportional to the length of the mutated versions of gene H. This shows that the tail length is measured by the length of gene H protein (gpH), which seems to be approximately as long as the tail tube, if extended like a thread, according to secondary structure prediction (α-helices connected by other structures). Various pieces of evidence show that about six molecules of gpH are attached to the remaining portion of the initiator by the C-terminal part and folded into a somewhat compact form, while they are elongated as they are enclosed in the tail tube during assembly of gpV. Unlike interaction between the length-measuring genome RNA and the coat protein of tobacco mosaic virus, the major tail protein gpV does not bind specifically to the ruler protein gpH. Rather, gpH determines the tail length by inhibiting the binding of gpU to short tails and by signalling the pause when the correct tail length is attained.     

Evolution of the structure of tail feathers: implications for the theory of sexual selection

Bird tails are extraordinarily variable in length and functionality. In some species, males have evolved exaggeratedly long tails as a result of sexual selection. Changes in tail length should be associated with changes in feather structure. The study of the evolution of feather structure in bird tails could give insight to understand the causes and means of evolution in relation to processes of sexual selection. In theory, three possible means of tail length evolution in relation to structural components might be expected: (1) a positive relationship between the increase in length and size of structural components maintaining the mechanical properties of the feather; (2) no relationship; that is, enlarging feather length without changes in the structural components; and (3) a negative relationship; that is, enlarging feather length by reducing structural components. These hypotheses were tested using phylogenetic analyses to examine changes in both degree of exaggeration in tail length and structural characteristics of tail feathers (rachis width and density of barbs) in 36 species, including those dimorphic and nondimorphic in tail length. The degree of sexual dimorphism in tail length was negatively correlated with both rachis width and density of barbs in males but not in females. Reinforcing this result, we found that dimorphism in tail length was negatively associated with dimorphism in tail feather structure (rachis width and density of barbs). These results support the third hypothesis, in which the evolution of long feathers occurs at the expense of making them simpler and therefore less costly to produce. However, we do not know the effects of enfeeblement on the costs of bearing. If the total costs increased, the enfeeblement of feathers could be explained as a reinforcement of the honesty of the signal. Alternatively, if total costs were reduced, the strategy could be explained by cheating processes. The study of female preferences for fragile tail feathers is essential to test these two hypotheses. Preferences for fragile tails would support the evolution of reinforcement of honesty, whereas female indifference would indicate the existence of cheating in certain stages of the evolutionary process.     

Some Bacteriophages Active Against Rhizobium trifolii Strain W19

Fourteen soil bacteriophages active against Rhizobium trifolii W19 have been studied which fall into four structural groups. Group 1 phages have contractile tails. Some particles show double base plates to which at least three spikes are attached, and fibers are attached to the base plates. Group 2 phages also have contractile tails. At least five spikes are attached to the base plate, and there are spherical bodies adjacent to the tail, at the ends of fibers attached to the tail base. Group 3 phages have contractile tails, but are larger than phages of groups 1 and 2. The end of the tail has a complex structure. Group 4 phages have long, noncontractile tails.     

Extra-long bacteriophage T4 tails produced under in vitro conditions

Extra-long bacteriophage T4 tails have been produced under in vitro conditions from purified tails of normal length. These tails show a range of lengths suggesting that the basic increment of increased length is the 41 Å (Moody, 1971) axial repeating unit rather than the length of a normal tail. Some extra-long tails and tubes attached to baseplates show stain penetration down the central tunnel of the tube to approximately the normal tail length. The stain-penetrated tunnel, as visualised by three-dimensional reconstruction from the electron micrographs, has a diameter between 30 and 40 Å, sufficient to allow the passage of DNA. The exclusion of stain from the tunnel in the baseplate-near segment of the tube is interpreted as being due to the presence of additional material in the tunnel. The relevance of these observations to the assembly and length-regulation of the tail is discussed.     

A touch of glue to complete bacteriophage assembly: the tail‐to‐head joining protein (THJP) family

Bacteriophage SPP1 is a nanomachine built to infect the bacterium Bacillus subtilis. The phage particle is composed of an icosahedric capsid, which contains the viral DNA, and a long non‐contractile tail. Capsids and tails are produced in infected cells by two distinct morphogenetic pathways. Characterization of the suppressor‐sensitive mutant SPP1sus82 showed that it produces DNA‐filled capsids and tails but is unable to assemble complete virions. Its purified tails have a normal length but lack a narrow ring that tapers the tail end found at the tail‐to‐head interface. The mutant is defective in production of gp17. The gp17 ring is exposed in free tails competent for viral assembly but becomes shielded in the final virion structure. Recombinant gp17 is active in an in vitro assay to stick together capsids and tails present in extracts of SPP1sus82‐infected cells, leading to formation of infectious particles. Gp17 thus plays a fundamental role in the tail‐to‐head joining reaction, the ultimate step of virus particle assembly. This is the conserved function of gp17 and its structurally related proteins like lambda gpU. This family of proteins can also provide fidelity to termination of the tail tube elongation reaction in a subset of phages including coliphage lambda.     

Electron microscopy of virulent phages for Streptococcus lactis.

Electron microscopic studies were made on eight virulent Streptococcus lactis bacteriophages. These phages were taken as representative of eight host range groups established in a study of 75 phage isolates and 253 hosts (213 S. lactis, 22 S. cremoris, 18 S. diacetilactis). The phages studied were shown to have an isometric hexagonal head and noncontractile tails, usually several times longer than the head diameter. The virus heads were octahedral. The phages investigated represented three morphological types on the basis of head diameter , tail thickness, and tail length. These dimensions were approximately: for type I phages, 63, 172, and 11 nm, respectively; type II, 73, 200, and 20 nm, respectively; and type III, represented here by a single phage, 98, 551, and 12 nm, respectively. The tail surface revealed a different arrangment of the structural subunits which lent a helical appearance to the tails of type I and II phages and a guaffered tube appearance to the tail of type III phage. The number of turns along the tail axis, turn length, axial pitch, and helix angle were: type I, 32, 12 to 13 nm, 7.14 nm, and 11 degrees 43', respectively; type II, 24, 24, to 28 nm, 40.00 nm, and 32 degrees 30', respectively; and type III, 120, 12 nm, and no visible slope towards the axis. The morphology types showed complete correlation with serological groups, but not with groups based on host range pattern.     

Electron microscopy and structural model of human fibronectin receptor.

Highly-purified human fibronectin receptor (a heterodimer of two distinct subunits, alpha and beta) was studied using electron microscopy and a variety of preparative procedures. It was found that the receptor consists of a globular head approximately 80 by 120 A and two tails about 20 A thick and 180-200 A long. The whole complex is approximately 280 A long. At low concentrations of detergent the receptor forms doublets, triplets or rosettes associated with the tails which possess the transmembrane portion of the molecule. Computer-assisted structure prediction using the published amino acid sequence of both subunits showed differences in the secondary structure of the tails, the alpha-tail being rich in beta-strands, the beta-tail having five cysteine-rich repeats analogous to the EGF-like repeats of laminin. Estimates of the length of the tails from the predicted structure conformed well with the dimensions obtained from electron micrographs.     

Single molecule studies of physiologically relevant telomeric tails reveal POT1 mechanism for promoting G-quadruplex unfolding

Human telomeres are composed of duplex TTAGGG repeats and a 3' single-stranded DNA tail. The telomeric DNA is protected and regulated by the shelterin proteins, including the protection of telomeres 1 (POT1) protein that binds telomeric single-stranded DNA. The single-stranded tail can fold into G-quadruplex (G4) DNA. Both POT1 and G4 DNA play important roles in regulating telomere length homeostasis. To date, most studies have focused on individual quadruplexes formed by four TTAGGG repeats. Telomeric tails in human cells have on average six times as many repeats, and no structural studies have examined POT1 binding in competition with G4 DNA folding. Using single molecule atomic force microscopy imaging, we observed that the majority of the telomeric tails of 16 repeats formed two quadruplexes even though four were possible. The result that physiological telomeric tails rarely form the maximum potential number of G4 units provides a structural basis for the coexistence of G4 and POT1 on the same DNA molecule, which is observed directly in the captured atomic force microscopy images. We further observed that POT1 is significantly more effective in disrupting quadruplex DNA on long telomeric tails than an antisense oligonucleotide, indicating a novel POT1 activity beyond simply preventing quadruplex folding.     

The role of structural changes in T4 bacteriophage tail proteins

Conformational changes in bacteriophage tail proteins after heating and ionic strength alteration leading to dissociation of tail sheath have been studied using protein fluorescence, differential scanning microcalorimetry and electron microscopy methods. Autonomous structural changes in tube-baseplate proteins have been revealed. They take place under the same conditions as those which release the bonds holding the sheath protein subunits to those of the tube in isolated sheathed tails. The conformational changes in the tube-baseplates are reversible similarly to the process of assembly and disassembly of the extended sheath. Morphological changes in the tube have been found at the temperature above the transition registered by protein fluorescence but not by calorimetry. This suggests that revealed spectral alterations reflect changes in quaternary structure of tail tube in particular.     

A complex containing the CCR4 and CAF1 proteins is involved in mRNA deadenylation in Drosophila

The CCR4-NOT complex is the major enzyme catalyzing mRNA deadenylation in Saccharomyces cerevisiae. We have identified homologs for almost all subunits of this complex in the Drosophila genome. Biochemical fractionation showed that the two likely catalytic subunits, CCR4 and CAF1, were associated with each other and with a poly(A)-specific 3' exonuclease activity. In Drosophila, the CCR4 and CAF1 proteins were ubiquitously expressed and present in cytoplasmic foci. Individual knock-down of several potential subunits of the Drosophila CCR4-NOT complex by RNAi in tissue culture cells led to a lengthening of bulk mRNA poly(A) tails. Knock-down of two individual subunits also interfered with the rapid deadenylation of Hsp70 mRNA during recovery from heat shock. Similarly, ccr4 mutant flies had elongated bulk poly(A) and a defect in Hsp70 mRNA deadenylation. A minor increase in bulk poly(A) tail length was also observed in Rga mutant flies, which are affected in the NOT2 subunit. The data show that the CCR4-NOT complex is conserved in Drosophila melanogaster and plays a role in general and regulated mRNA deadenylation.     

Chaperone–Protein Interactions That Mediate Assembly of the Bacteriophage Lambda Tail to the Correct Length

Bacteriophage λ makes two proteins with overlapping amino acid sequences that are essential for tail assembly. These two proteins, gpG and gpGT, are related by a programmed translational frameshift that is conserved among diverse phages and functions in λ to ensure that gpG and the frameshift product gpGT are made in a molar ratio of approximately 30:1. Although both proteins are required and must be present in the correct ratio for assembly of functional tails, neither is present in mature tails. During λ tail assembly, major tail protein gpV polymerizes to form a long tube whose length is controlled by the tape measure protein gpH. We show that the “G” domains of gpG and gpGT bind to all or parts of tail length tape measure protein gpH and that the “T” domain of gpGT binds to major tail shaft subunit gpV, and present a model for how gpG and gpGT chaperone gpH and direct the polymerization of gpV to form a tail of the correct length.     

Biogenesis of a Bacteriophage Long Non-Contractile Tail

Siphoviruses are main killers of bacteria. They use a long non-contractile tail to recognize the host cell and to deliver the genome from the viral capsid to the bacterial cytoplasm. Here, we define the molecular organization of the Bacillus subtilis bacteriophage SPP1 ~ 6.8 MDa tail and uncover its biogenesis mechanisms. A complex between gp21 and the tail distal protein (Dit) gp19.1 is assembled first to build the tail cap (gp19.1-gp21Nter) connected by a flexible hinge to the tail fiber (gp21Cter). The tip of the gp21Cter fiber is loosely associated to gp22. The cap provides a platform where tail tube proteins (TTPs) initiate polymerization around the tape measure protein gp18 (TMP), a reaction dependent on the non-structural tail assembly chaperones gp17.5 and gp17.5* (TACs). Gp17.5 is essential for stability of gp18 in the cell. Helical polymerization stops at a precise tube length followed by binding of proteins gp16.1 (TCP) and gp17 (THJP) to build the tail interface for attachment to the capsid portal system. This finding uncovers the function of the extensively conserved gp16.1-homologs in assembly of long tails. All SPP1 tail components, apart from gp22, share homology to conserved proteins whose coding genes’ synteny is broadly maintained in siphoviruses. They conceivably represent the minimal essential protein set necessary to build functional long tails. Proteins homologous to SPP1 tail building blocks feature a variety of add-on modules that diversify extensively the tail core structure, expanding its capability to bind host cells and to deliver the viral genome to the bacterial cytoplasm.     

The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteria

The contractile tail of bacteriophage T4 is a molecular machine that facilitates very high viral infection efficiency. Its major component is a tail sheath, which contracts during infection to less than half of its initial length. The sheath consists of 138 copies of the tail sheath protein, gene product (gp) 18, which surrounds the central non‐contractile tail tube. The contraction of the sheath drives the tail tube through the outer membrane, creating a channel for the viral genome delivery. A crystal structure of about three quarters of gp18 has been determined and was fitted into cryo‐electron microscopy reconstructions of the tail sheath before and after contraction. It was shown that during contraction, gp18 subunits slide over each other with no apparent change in their structure.     

The tail structure of bacteriophage T4 and its mechanism of contraction

Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail assembly at 15-A resolution shows the hexagonal dome-shaped baseplate, the extended contractile sheath, the long tail fibers attached to the baseplate and the collar formed by six whiskers that interact with the long tail fibers. Comparison with the structure of the contracted tail shows that tail contraction is associated with a substantial rearrangement of the domains within the sheath protein and results in shortening of the sheath to about one-third of its original length. During contraction, the tail tube extends beneath the baseplate by about one-half of its total length and rotates by 345 degrees , allowing it to cross the host's periplasmic space.     

Three-dimensional structure of bacteriophage T4 baseplate

The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three-dimensional structure of the baseplate-tail tube complex determined to a resolution of 12 A by cryoelectron microscopy. The baseplate has a six-fold symmetric, dome-like structure approximately 520 A in diameter and approximately 270 A long, assembled around a central hub. A 940 A-long and 96 A-diameter tail tube, coaxial with the hub, is connected to the top of the baseplate. At the center of the dome is a needle-like structure that was previously identified as a cell puncturing device. We have identified the locations of six proteins with known atomic structures, and established the position and shape of several other baseplate proteins. The baseplate structure suggests a mechanism of baseplate triggering and structural transition during the initial stages of T4 infection.     

Novel structural elements identified during tail resorption in Xenopus laevis metamorphosis: lessons from tailed frogs.

When the tail of the Xenopus laevis tadpole resorbs at the end of metamorphosis, various cell types, including muscle, fibroblasts, skin, and spinal cord, are lost at about the same time. However, feeding frogs with tails can be produced by inhibiting thyroid hormone production at the climax of metamorphosis with the goitrogen methimazole. These tails lose their fast muscle preferentially, showing that the different cell types of the tail have different fates and confirming that more than one cell death program is involved in tail resorption. Both normal and methimazole tails contain "cords," novel structures that consist of two dorsal and two ventral parallel rows of slow muscle bundles joined by collagen fibers that run the length of the tail. The cords persist until the very end of tail resorption, being the last structure to dissolve. When thyroid hormone induces expression of proteolytic enzymes in the notochord sheath, the notochord, a structural rod that runs the length of the tail, begins to buckle, demonstrating that the tail is under tension. When sections of the tail that contain cords are surgically separated from the notochord, they contract in vitro, suggesting that the cords contribute to the tension that augments tail resorption.     

The lambda head-tail joining reaction: purification, properties and structure of biologically active heads and tails

Procedures were developed to obtain biologically active lambda heads and tails at high purity with 20 to 40% recovery. Free heads, free tails and phage particles differ markedly in stability. Phage are stable in solutions containing Mg²⁺ but tails are not. The protein subunits which form the shaft of the tail dissociate in the presence of Mg²⁺ and form multisubunit spherical structures. EDTA protects free tails against inactivation but disrupts heads and phage particles. The four carbon diamine, putrescine, stabilizes heads against inactivation; the three and five carbon diamines are less effective. Electron micrographs reveal a new “knob” structure at the distal end of the tail fiber of phage and of free tails. Tails released from EDTA-disrupted phage possess a “head-tail connector”, a structure not present on the tail before its joining with a head.     

Slo1 tail domains,but not the Ca2+ bowl,are required for the beta 1 subunit to increase the apparent Ca2+ sensitivity of BK channels

Functional large-conductance Ca(2+)- and voltage-activated K(+) (BK) channels can be assembled from four alpha subunits (Slo1) alone, or together with four auxiliary beta1 subunits to greatly increase the apparent Ca(2+) sensitivity of the channel. We examined the structural features involved in this modulation with two types of experiments. In the first, the tail domain of the alpha subunit, which includes the RCK2 (regulator of K(+) conductance) domain and Ca(2+) bowl, was replaced with the tail domain of Slo3, a BK-related channel that lacks both a Ca(2+) bowl and high affinity Ca(2+) sensitivity. In the second, the Ca(2+) bowl was disrupted by mutations that greatly reduce the apparent Ca(2+) sensitivity. We found that the beta1 subunit increased the apparent Ca(2+) sensitivity of Slo1 channels, independently of whether the alpha subunits were expressed as separate cores (S0-S8) and tails (S9-S10) or full length, and this increase was still observed after the Ca(2+) bowl was mutated. In contrast, beta1 subunits no longer increased Ca(2+) sensitivity when Slo1 tails were replaced by Slo3 tails. The beta1 subunits were still functionally coupled to channels with Slo3 tails, as DHS-I and 17 beta-estradiol activated these channels in the presence of beta1 subunits, but not in their absence. These findings indicate that the increase in apparent Ca(2+) sensitivity induced by the beta1 subunit does not require either the Ca(2+) bowl or the linker between the RCK1 and RCK2 domains, and that Slo3 tails cannot substitute for Slo1 tails. The beta1 subunit also induced a decrease in voltage sensitivity that occurred with either Slo1 or Slo3 tails. In contrast, the beta1 subunit-induced increase in apparent Ca(2+) sensitivity required Slo1 tails. This suggests that the allosteric activation pathways for these two types of actions of the beta1 subunit may be different.     

Plasticity in courtship and sneaking behaviors depending on tail length in the male guppy, <Emphasis Type="Italic">Poecilia reticulata</Emphasis>

Male guppies Poecilia reticulata exhibit two types of mating behavior, i.e., courtship displays for cooperative copulation and sneaking attempts for forced copulation. The frequencies of the two male mating behaviors are influenced by tail length. Males possessing long tails exhibit courtship displays less frequently and sneaking attempts more frequently than those possessing short tails, even though they have similar total lengths. To examine whether these male behavioral tendencies depending on tail length are genetically controlled or are determined by tail length per se, tail length manipulation was conducted. The tail lengths of males that had previously possessed longer tails were surgically shortened to a greater degree than those of their counterparts that had previously possessed shorter tails. Although the frequencies of the mating behaviors exhibited by the latter males did not apparently change, the former males clearly increased the frequency of courtship displays and decreased that of sneaking attempts following tail shortening. These results indicate that males adjust the frequencies of the two mating behaviors according to their tail length. Since females avoid cooperative mating with males possessing long tails, the change in mating behavioral patterns by males depending on their tail length may increase their mating opportunities.