The wrapping phenomenon in air-dried and negatively stained preparations

We demonstrate that the interface energies involved in the direct preparation of supramolecular structures onto supporting films leads very frequently to a smooth wrapping of the supporting film around approximately one third to one half of the structure. We conclude that in such cases the structure is more rigid than the supporting film; examples being ribosomes, small viruses and small glass fragments. Other structures are less rigid and become significantly flattened. Complete flattening is frequently observed with empty virus capsids. The sandwich technique, by which a specimen is placed between two supporting films, in general leads to increased flattening. Only in few cases (e.g. ribosomes) are biological particles rigid enough to resist flattening and become wrapped from both sides.

Mechanism of coliphage M13 contraction: intermediate structures trapped at low temperatures

The filamentous coliphage M13 can be transformed into a spherical particle (termed spheroid) by exposure to an interface of water and slightly polar but hydrophobic solvent such as chloroform-water at 24 degrees C. We report here that exposure of M13 filaments to a chloroform-water interface at 2 degrees C trapped the phage particles in forms morphologically intermediate to filaments and spheroids. These structures were rods 250 nm long and 15 nm wide, and each had a closed, slightly pointed end, an open flaired end, and a hollow central channel. The final contraction of these intermediates (termed I-forms) into spheroids was dependent upon both temperature and the presence of the solvent-water interface but was apparently independent of both the minor phage coat proteins and the virion DNA. Although stable in an aqueous environment, I-forms, in contrast to filaments, were readily disrupted by detergents, suggesting that the phage structure had been altered to a form more easily solubilized by membrane lipids. These solvent-induced changes might be related to the initial steps of phage penetration in vivo.

Comparison of the lipid-containing bacteriophages PRD1, PR3, PR4, PR5 and L17

Five broad host range lipid-containing bacteriophages PRD1, PR3, PR4, PR5 and L17 isolated from different parts of the world were compared using biological and structural criteria. Virus morphology as well as genome sizes appeared to be identical. However, these viruses could be distinguished by restriction endonuclease mapping and by their structural protein patterns in SDS--gel electrophoresis. The viruses studied thus form a very close group of lipid-containing bacteriophages. We suggest PRD1 as a model organism for this group and that the group be called the PRD1 phage group.

Structure and architecture of the bacterial virus fd. An infrared linear dichroism study

Oriented gels of intact bacterial virus fd have been invetigated by infrared linear dichroism. Infrared absorption band maxima and dichroism indicate an alpha-helix content of the major coat protein of 95-100%. The alpha-helical rods of the coat protein are aligned parallel to the long axis of the virion with an inclination roughly estimated to approximately 37 degree. The presence of DNA infrared bands at 968, 885, 830 and 799 cm-1, the absence of a band at 860 cm-1 and the perpendicular polarization of the symmetric PO-2 stretching vibration at 1085 cm-1 are all indicative of a B-type backbone conformation in the single-stranded DNA. We find no evidence for specific interaction between aromatic side groups (phenylalanine, tyrosine) and the DNA bases. Our results independently confirm most features of the model of Marvin and co-workers [2,15 ] based on low-resolution X-ray diffraction studies. However, our findings contradict their suggestion of an A-type DNA in the bacterial virus fd. Two results are consistent with rigid and stable order in the virus. First, over a 4-day period, 65% of the peptide hydrogens remain unexchanged with deuterium. Second, changes in the relative humidity of the sample do not result in any shifts in the DNA spectrum that are characteristic of free DNA.

Knotted DNA from bacteriophage capsids

The majority of the DNA prepared from tailless capsids of bacteriophage P2 by the phenol extraction procedure consists of monomeric rings that have their cohesive ends joined. Electron microscopic and ultracentrifugal studies indicate that these molecules have a complex structure that is topologically knotted; they have a more compact appearance and a higher sedimentation coefficient when compared with regular nicked P2 DNA rings. Linearization of these rings by thermal dissociation or repair of the cohesive ends by DNA polymerase I in the presence of all four deoxynucleoside triphosphates gives molecules that are indistinguishable from normal P2 DNA that has been similarly treated. The knotted nature of the majority of P2 head DNA is further supported by analyzing the products when these molecules are treated with ligase and the ligase-treated molecules are subsequently nicked randomly with DNase I. The data are consistent with the notion that, if such a molecule is first converted to a form that contains only one single-chain scission per molecule, strand separation gives a linear strand and a highly knotted single-stranded ring. The results suggest that the DNA packaged in tailless P2 capsids is arranged in a way that leads to the formation of a complex knot when the ends join. In an intact phage particle, the anchoring of one terminus of the DNA to the head-proximal end of the tail [Chattoraj, D. K. & Inman, R. B. (1974) J. Mol. Biol. 87, 11-22] presumably diminishes or prevents this kind of joining. The novel knotted DNA can be used to assay type II DNA topoisomerases that break and rejoin DNA in a double-stranded fashion.

Filamentous bacteriophage contract into hollow spherical particles upon exposure to a chloroform-water interface

The bacteriophage M13 is a 1 micrometer long filament consisting of a circular single-stranded DNA loop firmly held within a tubular protein and capsid. We report here that exposure to a chloroform-water interface initiates a 20 fold contraction of each filament into a hollow protein sphere. In these 0.04 micrometer diameter particles, termed M13 "spheroids," two thirds of the DNA is apparently extruded through a hole in the wall of the spheroid; the portion of DNA remaining inside the shell centers about the origins of M13 DNA replication. These results suggest that the filament, upon exposure to a membrane environment, undergoes an ordered change whereby the DNA is released into the cell and the coat protein is changed to a form more easily solubilized by the membrane lipids.

Hydrogen-1 and carbon-13 nuclear magnetic resonance of the aromatic residues of fd coat protein

The aromatic residues of fd coat protein in sodium dodecyl sulfate micelles are characterized by 1H and 13C NMR. Resonances from both types of nuclei show structure-induced chemical shift dispersion and line widths indicative of a folded native structure for the protein. The two tyrosines were found to have pKas of 12.3 and 12.5 by 1H NMR and spectrophotometric titrations. 13C relaxation measurements show that two of the three Phe rings have significant internal mobility, the two Tyr rings have moderate internal mobility, and the Trp side chain is completely immobilized. Qualitative comparisons are made between the intact virus and the isolated coat protein.

Phosphorus-31 nuclear magnetic resonance of fd virus

31P NMR experiments on the filamentous bacteriophage fd are used to characterize the viral DNA. Because fd is a 16.4 X 10(6) dalton rod-shaped particle, methods of high-resolution solid-state NMR including cross polarization, proton decoupling, and magic angle sample spinning are utilized. The 31P chemical shielding tensor of solid fd is indistinguishable from that of single-stranded or double-stranded DNA in the absence of proteins; therefore the 31P chemical shift does not show evidence of structural changes in DNA upon incorporation into the virus. fd in solution has a very broad 31P resonance line width. The line width is due to static chemical shift anisotropy that is not motionally averaged, as shown by the generation of sidebands with magic angle sample spinning and a linear dependence of line width on magnetic field strength. These results indicate that DNA packaged inside fd is immobilized by the coat proteins.

Structure of the filamentous bacteriophage fl. Location of the A, C, and D minor coat proteins

The location within the virion of the A, C, and D minor coat proteins of the filamentous bacteriophage fl has been analyzed. The A protein is present in approximately 5 copies/particle and is located at the tip of normal length phage, miniphage, and fl/pBR322 chimeric phage, a longer than normal length phage. The mole ratios of the A, C, and D proteins are the same for each type of particle, consistent with a model of phage organization in which the minor coat proteins are clustered near or at the ends of the phage. Normal length phage were fragmented by passing them through a French press, and those fragments that contained the A protein were separated from those that did not by treating the mixture with anti-A protein antibody. Analysis of the protein compositions of the two populations of fragments showed that the A and D proteins were found together in one population of fragments and that most, it not all, of the C protein was found in the other. These results show that the D protein is located near or at the A protein end of the phage and that the C protein is located in a region near or at the opposite end. Treatment of the virion with proteases which lowered the infectivity of the phage resulted in particles in which only the A protein was cleaved to any detectable extent. These particles remained resistant to the action of micrococcal nuclease.

Genes VI, VII and IX of bacteriophage M13: identification of their products as minor capsid proteins

In earlier work, two new minor capsid proteins of molecular weight 3500 (C-protein) and 11,500 (D-protein) were detected in M13 virions. To determine their genetic origin, differential amino acid labeling, amino acid analysis and Edman degradation analysis were performed on these proteins. The data demonstrate that D-protein is the product of gene VI whereas C-protein is composed of both the proteins specified by gene VII and the recently discovered gene IX. by selective labeling with arginine, the number of C and D protein molecules present in M13 virions was estimated to be 5 D-protein and approx. 6-8 C-protein molecules. From synthesis studies of C-protein in E. coli minicells which harbor either wt- or amber mutant RF molecules, evidence is presented that genes V, VII and IX form an operon.

Mutator bacteriophage D108 and its DNA: an electron microscopic characterization

Three types of phage particles were observed on CsCl step gradients when D108 was purified from lysates prepared by induction of a prophage. These particle types were identified to be the mature phage, tailless DNA-filled heads, and a form of nucleoprotein aggregates. The nucleoprotein aggregates banded at a density (rho) of greater than 1.6. DNA molecules isolated from mature phage particles were (38.305 +/- 1.226) kilobases (kb) in length. Denaturation and renaturation of D108 DNA resulted in the formation of linear double-stranded molecules with variable-length single-stranded tails at one end. About 30% of the annealed molecules also carried an internal nonhomology, which was shown to be the region called the G-loop in Mu and P1 DNAs. Following the notation used for different regions of denatured, annealed Mu DNA, we measured the lengths of the equivalent D108 DNA regions to be as alpha-D108 = (32.178 +/- 1.370) kb; G-D108 = (3.07 +/- 0.382) kb; beta-D108 = (2.291 +/- 0.306) kb; SE-D108 = (0.966 +/- 0.433) kb. Formation of D108; Mu heteroduplexes disclosed the presence of five nonhomologies, two of which were partial. One of the partial heterologies was in the G-loop region. The largest nonhomology, (1.393 +/- 0.185) kb in size, was near the c end (immunity region) and probably spans the c and the ner genes of Mu. beta-D108 was shown to carry a (0.556 +/- 0.097)-kb insertion close to its right end. A short 100-base-pair region appeared to have been conserved at the ends of D108 and Mu. Occasionally, a 50-to 100-base-pair-long unpaired region was also observed at the left end of D108: Mu heteroduplexes. These sequences were presumably of bacterial DNA. Taken together, our results complement and extend our earlier genetic studies which established that D108 was a mutator phage heteroimmune to Mu with a host range different from Mu's.

Bacteriophage T4 morphogenesis as a model for assembly of subcellular structure

The sequence of steps in bacteriophage T4 assembly has been elucidated by using a combination of genetic, biochemical, and ultrastructural techniques. The phage head, tail, and tail fibers are assembled via independent pathways, and then are jointed to form the complete virus. Current knowledge of these three pathways is reviewed briefly. Two general insights emerging from phage assembly studies are (1) a realization of the importance of kinetic controls, and (2) recognition of the role of nonstructural accessory proteins in assembly. Controls of protein association rates by a proposed heterocooperation mechanism can account for the strict sequential ordering of steps in complex self-assembly pathways such as that of T4 tail assembly. The same mechanism can explain how proteins capable of polymorphic assembly are induced to form correct structures rather than aberrant ones of similar stability. Nonstructural accessory proteins provide additional means for enhancing rates of interactions of specific structural proteins by mechanisms that may be analogous to those of enzyme catalysis. The insights gained from bacteriophage assembly probably apply to organellogenesis in general.

Scaffolding proteins and the genetic control of virus shell assembly

Historically a gap has existed between the study of the one-dimensional organization of hereditary information in genes, and of the three-dimensional organization of macromolecules in biological structures. In this article we describe progress in closing this gap through the genetic and biochemical analysis of the assembly of the icosahedral shells of spherical viruses, a class of subcellular structures whose subunit organization is relatively well understood. The genes specifying the proteins required for capsid assembly have been identified for many bacterial viruses. By using mutants defective in these genes, it has been possible to identify intermediates in shell morphogenesis and DNA condensation, and to unravel the different levels of the genetic control of macromolecular assembly processes. In general, a precursor shell or procapsid is first constructed, and the DNA is subsequently coiled within it. The construction of a closed shell poses as difficult a problem for a virus as for an architect. In the well-studied bacteriophage P22 of Salmonella typhimurium, the construction of the procapsid requires the interaction of about 200 molecules of the gene-8 scaffolding protein with 420 molecules of the gene-5 coat protein, forming a double-shelled structure with the scaffolding protein on the inside. Once completed, procapsids undergo substantial alteration in the course of encapsulating the viral DNA. In P22, the initiation of DNA packaging triggers the exit of all of the scaffolding molecules from within the capsid, probably through the coat-protein lattice. These released molecules are re-utilized, interacting with newly synthesized coat subunits to form further procapsids. Thus, the scaffolding protein functions catalytically in capsid assembly. All of the well-studied DNA phages require a scaffolding protein species for procapsid assembly, though their properties vary. Purified coat and scaffolding subunits by themselves show little tendency to polymerize, and are stable as monomers in solution. Upon mixing together under the appropriate conditions, however, the proteins copolymerize into double shells. Their interaction with each other appears to be critical for efficient assembly; this interaction probably occurs on the edges of growing shells, and not among subunits in solution. We have termed this kind of process, which we previously described in T4 tail morphogenesis, self-regulated assembly. The subunits are synthesized in a nonreactive form and are activated, not in solution, but upon incorporation into the growing substrate structure. A number of further transformations of the capsid subunits occur only within the organized structure and not as free subunits. Thus, aspects of the genetic information controlling the assembly process are not fully expressed at the level of the properties of protein subunits, but become manifest only through interactions with other proteins, or at a higher level, after completion of the correct organized structure.

Nuclear magnetic resonance of the filamentous bacteriophage fd

The filamentous bacteriophage fd and its major coat protein are being studied by nuclear magnetic resonance (NMR) spectroscopy. 31P NMR shows that the chemical shielding tensor of the DNA phosphates of fd in solution is only slightly reduced in magnitude by motional averaging, indicating that DNA-protein interactions substantially immobilize the DNA packaged in the virus. There is no evidence of chemical interactions between the DNA backbone and the coat protein, since experiments on solid virus show the 31P resonances to have the same principle elements of its chemical shielding tensor as DNA. 1H and 13C NMR spectra of fd virus in solution indicate that the coat proteins are held rigidly in the structure except for some aliphatic side chains that undergo relatively rapid rotations. The presence of limited mobility in the viral coat proteins is substantiated by finding large quadrupole splittings in 2H NMR of deuterium labeled virions. The structure of the coat protein in a lipid environment differs significantly from that found for the assembled virus. Data from 1H and 13C NMR chemical shifts, amide proton exchange rates, and 13C relaxation measurements show that the coat protein in sodium dodecyl sulfate micelles has a native folded structure that varies from that of a typical globular protein or the coat protein in the virus by having a partially flexible backbone and some rapidly rotating aromatic rings.

Bacteriophage K7, a double stranded DNA phage that infects strains of Escherichia coli harbouring drug resistance factors of incompatability group W

Bacteriophage K7 is specific for Escherichia coli strains harbouring R factors of incompatability group W, including hybrid coliphage P1-Myxococcus virescens plasmids. The phage has an unusual morphology with an isometric head and long tail of variable length. The tail lengths appear to fall into classes corresoonsing to simple multimers of a unit length. Partially purified lysates of the phage include material that may represent phage particles in the process of biogenesis and other material demonstrating attachment of phage to cell envelope. Newly released phage DNA contains single standed ends. In the course of work. E. coli strains that harbour R factor Sa were found to be apparently restrictive.

Turbidity measurements in an analytical ultracentrifuge. Determinations of mass per length for filamentous viruses fd, Xf, and Pf3

An analytical ultracentrifuge has been used to measure light-scattering intensities by the transmittance method. The technique, which is applicable to particles of many sizes and shapes, has the principal advantage that samples can be kept free of dust during the measurements. Also, sample volumes are small, and the scanner and interference optics can be used simultaneously to obtain, for a given sedimenting boundary, turbidity steps at different wavelengths and the concentration step. In the present application the data yield mass per length estimates for three filamentous viruses, 19 100 daltons/nm for fd, 19 600 daltons/nm for Pf3, and 19 100 daltons/nm for Xf.

Coliphage HK243: biological and physicochemical characteristics

Coliphage HK243 can form plaques on Escherichia coli C and K-12, but not B. The plaques are 1-2 mm in diameter and are opaque areas which clear upon exposure to chloroform vapor. During one-step growth, the eclipse and the latent periods are 20 and 30 min, respectively. Phage-infected cells continue to produce cell-free plaque-forming units for as long as 80 min after the end of the latent period, although at high multiplicities of infection (MOI) most cells lyse. No lysogenic bacteria have been found among survivors, so HK243 is considered a virulent phage. Some of the cells surviving a high MOI challenge are maltose negative and resistant to both HK243 and coliphage lambda. This fact has made possible the isolation of lambda-resistant mutants of lambda-lysogens. However, no serological cross-reaction between the phages lambda and HK243 has been detected. Genetic data involving three essential loci and a locus controlling plaque morphology suggest a circular linkage map. The virions are tadpole-shaped with an icosahedral head 68 nm long which is attached to a flexible tail 131 nm long. The phage has a linear, duplex DNA genome of molecular weight approximately 44 x 10(6) and a base composition of 33% adenine, 31% thymine, 16% guanine, and 20% cytosine.

Temperate coliphages: classification and correlation with habitats

Temperate coliphages were recovered from sewage, mammalian feces, and lysogenic strains of Escherichia coli. A total of 32 phages of independent origin were divided into six groups by applying the criteria of host range, antigenic homology, and the ultraviolet inducibility of the prophage. The demonstration of genetic interactions in some cases has confirmed the classification scheme. Nine phages were assigned to the P2 family and 19 to the lambda family. The remaining four isolates may represent some novel phylogenetic types. Phages recovered from the lysogenic strains of E. coli were all found to be P2 related, whereas a majority of the phages recovered as cell-free plaque-forming units were assignable to the lambda family. It is proposed that the biological attributes of the phages belonging to the two principal families are reflected in the distribution patterns observed. The virions of phage HK256 show multiple tail fibers and may thus represent a "new" virion form among the temperate coliphages.

Genetic analysis of bacteriophage P4 using P4-plasmid ColE1 hybrids

A set of plasmids that contain fragments of the bacteriophage P4 genome has been constructed by deleting portions of a P4-ColE1 hybrid. A P4 genetic map has been established and related to the physical map by examining the ability of these plasmids to rescue various P4 mutations. The P4 virl mutation and P4 genes involved in DNA replication (alpha), activation of P2 helper genes (delta and epsilon), polarity suppression (psu) and head size determination (sid) have been mapped, as has the region responsible for synthesis of a nonessential P4 protein. One of the deleted plasmids contains only 5900 base pairs (52%) of P4 but will form plaques if additional DNA is added to increase its total size to near that of P4. This plasmid is also unique in that it will not form stable associations with P2 lysogens of E. coli which are recA+. P4 alpha mutants can be suppressed as a result of replication under control of the ColE1 part of the hybrid.