Examination of the phosphate in conjugative F-like pili by use of electron spectroscopic imaging

F-like pili specified by conjugative plasmids have been reported to contain phosphate which may be noncovalently incorporated into the pilus. Electron spectroscopic imaging was able to detect phosphate in the filamentous, single-stranded DNA phage f1, used as positive control, but could not detect phosphate in F-like pili. Thus, the phosphate in purified pili which has been reported is probably derived from contaminating cell envelope material.

Raman spectroscopy of filamentous bacteriophage Ff (fd, M13, f1) incorporating specifically-deuterated alanine and tryptophan side chains. Assignments and structural interpretation

Structural interpretation of the Raman spectra of filamentous bacteriophages is dependent upon reliable assignments for the numerous Raman vibrational bands contributed from coat protein and packaged DNA of the virion. To establish unambiguous assignments and facilitate structural conclusions derived from them, we have initiated a systematic study of filamentous bacteriophage Ff (fd, f1, M13) incorporating protein subunits with specifically deuterated amino-acid side chains. Here, we report and interpret the Raman spectra of fd virions which incorporate: (a) a single deuterio-tryptophan residue per coat protomer [fd(Wd5)], (b) ten deuterio-alanines per protomer [fd(10Ad3)], and (c) both deuterio-tryptophan and deuterio-alanine [fd(Wd5 + 10Ad3)]. The unambiguous assignment of coat protein Raman bands in normal and deuterated isotopomers of fd establishes the validity of earlier empirical assignments of many key Raman markers, including those of packaged ssDNA (Thomas et al., 1988). Present results confirm that deoxyguanosine residues of the packaged ssDNA molecule depart from the usual C2'-endo/anti conformation characteristic of protein-free DNA in aqueous solution, although C2'-endo/anti conformers of thymidine are not excluded by the data. The combined results obtained here on normal fd, and on fd incorporating deuterio-tryptophan [fd(Wd5) and fd(Wd5 + 10Ad3)], show also that the microenvironment of the single tryptophan residue per coat protomer (W26) can be clearly deduced as follows: (a) The indole 1-NH donor group of each protomer in fd forms a moderately strong hydrogen bond, most likely to a hydroxyl oxygen acceptor. (b) The planar indole ring exists in a hydrophilic environment. (c) The torsion angle describing the orientation of the indole ring (C3-C2 linkage) with respect to the side-chain (C alpha-C beta bond) is unusually large, i.e., magnitude of X2,1 approximately 120 degrees. With respect to alanine isotopomers, the present results show that alanine residues, and possibly other methyl-containing side chains, are significant contributors to the fd Raman spectrum. The present study provides new information on protomer side chains of fd and demonstrates a Raman methodology which should be generally useful for investigating single-site interactions and macromolecular conformations in other nucleoprotein assemblies.

Secondary structure of coliphage Q beta RNA. Analysis by electron microscopy

The secondary structure of genomic RNA from the coliphage Q beta has been examined by electron microscopy in the presence of varying concentrations of spermidine using the Kleinschmidt spreading technique. The size and position of structural features that cover 70% of the viral genome have been mapped. The structural features that are visualized by electron microscopy in Q beta RNA are large. They range in size from 170 to 1600 nucleotides. A loop containing approximately 450 nucleotides is located at the 5' end of the RNA. It includes the initiation region for the viral maturation protein. A large hairpin containing approximately 1600 nucleotides is located in the center of the molecule. It is multibranched and includes most of the viral coat gene, the readthrough region of the A1 gene, and approximately one third of the viral replicase gene. Within the central hairpin, the initiation region for the viral replicase gene pairs with a region within the distal third of the viral coat gene. This structure may participate in the regulation of translational initiation of the viral replicase gene. Two structural variants of the central hairpin were observed. One of them brings the internal S and M viral replicase binding regions into juxtaposition. These observations suggest that the central hairpin may also participate in the regulation of translation of the viral coat gene. The secondary structures that are observed in Q beta RNA differ significantly from structures that we described previously in the genomic RNA of coliphage MS2 but are similar to structures we observed by electron microscopy in the related group B coliphage SP.

Bacteriophage HK97 structure: wholesale covalent cross-linking between the major head shell subunits

We describe initial genetic and structural characterizations of HK97, a temperate bacteriophage of Escherichia coli. We isolated 28 amber mutants, characterized them with respect to what phage-related structures they make, and mapped many of them to restriction fragments of genomic DNA. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of HK97 virions revealed nine different protein species plus a substantial amount of material that failed to enter the gel, apparently because it is too large. Five proteins are tail components and are assigned functions as tail fiber subunit, tail length template, and major shaft subunit (two and possibly three species). The four remaining proteins and the material that did not enter the gel are head components. One of these proteins is assigned as the portal subunit, and the remaining three head proteins in the gel and the material that did not enter the gel are components of the head shell. All of the head shell protein species have apparent molecular masses well in excess of 100 kDa; they share amino acid sequence with each other and also with a 42-kDa protein that is found in infected lysates and as the major component of prohead structures that accumulate in infections by one of the amber mutants. We propose that all of the head shell species found in mature heads are covalently cross-linked oligomers derived from the 42-kDa precursor during head shell maturation.

Retronphage phi R73: an E. coli phage that contains a retroelement and integrates into a tRNA gene

Some strains of Escherichia coli contain retroelements (retrons) that encode genes for reverse transcriptase and branched, multicopy, single-stranded DNA (msDNA) linked to RNA. However, the origin of retrons is unknown. A P4-like cryptic prophage was found that contains a retroelement (retron Ec73) for msDNA-Ec73 in an E. coli clinical strain. The entire genome of this prophage, named phi R73, is 12.7 kilobase pairs and is flanked by 29-base pair direct repeats derived from the 3' end of the selenocystyl transfer RNA gene (selC). P2 bacteriophage caused excision of the phi R73 prophage and acted as a helper to package phi R73 DNA into an infectious virion. The newly formed phi R73 closely resembled P4 as a virion and in its lytic growth. Retronphage phi R73 lysogenized a new host strain, reintegrating its genome into the selC gene of the host chromosome and enabling the newly formed lysogens to produce msDNA-Ec73. Hence, retron Ec73 can be transferred intercellularly as part of the genome of a helper-dependent retronphage.

Morphopoietic switch mutations of bacteriophage P2

During the growth of bacteriophage P4, for which the genome of bacteriophage P2 is needed as helper, the decision whether to make large, P2 size, heads or small, P4 size, heads depends on the size-directing function of P4's sid gene and on P2's "sid responsiveness." P2 mutants (=P2 sir) impaired in their response to P4's sid function are readily obtainable as one class of P2 plaque formers selected on certain P4 cl plasmid lysogens. We describe nine P2 sir mutants of independent origin. For eight we could assign their sir mutation to P2 gene N, which encodes the major capsid protein. DNA sequencing indicated an open reading frame of 357 codons for gene N and showed these sir mutations to affect only four codons within a 38-codon segment in the middle of N. Seven mutations are missense mutations (three of them identical); one is a deletion of one codon. There seems to be a correlation between the phenotypic "strength" of the sir mutations and the type of amino acid replacement by missense mutations. Although the weakest mutation, sir7, could not yet be assigned to any P2 gene, it appears clear from this work that P2's N gene product is the major (or only) target of P4's Sid gene function.

Physiological, morphological, and physicochemical characterization of a novel Escherichia coli bacteriophage, phage MM

A double-stranded DNA containing, T even-like, Escherichia coli bacteriophage, called MM, has been isolated from the local sewage and purified by polyethylene glycol precipitation followed by banding on a cesium chloride three-step gradient. It yields a burst size of 75 particles per infected cell, and has an adsorption coefficient of 3.3 x 10(-10) cm3/min and a latent period of 45 min. Electron microscopy of phage MM reveals an isometric icosahedral head, 92 nm long and 81 nm wide, and a 112-nm-long contractile tail with six pairs of 40-nm-long fibers attached to its baseplate. Phage MM appears similar to E. coli phage T4 or Salmonella phage O1. The density of phage MM in cesium chloride is 1.515 g/ml, and its total mass is 144 MDa. Gel electrophoresis of purified MM capsids displays two major capsid proteins in approximately equimolar amounts and with apparent molecular masses of 38 and 15 kDa. Similarly, purified MM tails yield two major polypeptides with apparent molecular masses of 55 and 16 kDa, most likely representing the major tail sheath and tail tube polypeptides. Its double-stranded DNA has a G-C content of 50%, a length of 131 kilobases (kb), and a mass of 89 MDa.

Regulation of filamentous bacteriophage length by modification of electrostatic interactions between coat protein and DNA

Bacteriophage fd gene VIII, which encodes the major capsid protein, was mutated to convert the serine residue at position 47 to a lysine residue (S47K), thereby increasing the number of positively charged residues in the C-terminal region of the protein from four to five. The S47K coat protein underwent correct membrane insertion and processing but could not encapsidate the viral DNA, nor was it incorporated detectably with wild-type coat proteins into hybrid bacteriophage particles. However, hybrid virions could be constructed from the S47K coat protein and a second mutant coat protein, K48Q, the latter containing only three lysine residues in its C-terminal region. K48Q phage particles are approximately 35% longer than wild-type. Introducing the S47K protein shortened these particles, the S47K/K48Q hybrids exhibiting a range of lengths between those of K48Q and wild-type. These results indicate that filamentous bacteriophage length (and the DNA packaging underlying it) are regulated by unusually flexible electrostatic interactions between the C-terminal domain of the coat protein and the DNA. They strongly suggest that wild-type bacteriophage fd makes optimal use of the minimum number of coat protein subunits to package the DNA compactly.

[Genetic control of resistance of Escherichia coli K12 to phage C1]

The bacteriophage C1 isolated in production cycle lysis belongs to the most common group of bacteriophages wide spread in nature and having the long noncontractile motile tail. Bacterial cells sensitivity to bacteriophage C1 is determined by functioning of the three different loci mapped in different regions of Escherichia coli map at 89, 75 and 61 min. The possibility of existence of a complex receptor for bacteriophage C1 is discussed.

Structure and assembly of bacteriophage PRD1, and Escherichia coli virus with a membrane

This article describes the structure and assembly of bacteriophage PRD1, a lipid-containing virus able to infect Escherichia coli. This phage, with an approximate diameter of 65 nm, is composed of an outer protein shell surrounding a lipid-protein membrane which, in turn, encloses the nucleic acid. The phage genome consists of a single linear dsDNA molecule of about 15 kb that has a protein covalently linked to each of its 5' ends. This protein is used as a primer in DNA replication. During assembly membrane proteins are inserted into the host cytoplasmic membrane while major capsid protein multimers are found in the cytoplasm. Capsid multimers, assisted by two nonstructural assembly factors, are capable of translocating the virus-specific membrane resulting in the formation of cytoplasmic empty particles. Subsequent DNA packaging leads to the formation of infections virus.

ESR of spin-labeled bacteriophage M13 coat protein in mixed phospholipid bilayers

Bacteriophage M13 major coat protein was spin-labeled with a nitroxide derivative of iodoacetamide, preferentially at the single methionine that is located in the hydrophobic region of the protein. The spin-labeled protein was incorporated at different lipid-to-protein ratios in phospholipid bilayers composed of dimyristoylphosphatidylglycerol (DMPG), dimyristoylphosphatidylcholine (DMPC), or the 1:1 molar mixture of these lipids. Both conventional and saturation transfer (ST) ESR studies were performed to investigate the rotational motions of the protein over a large dynamic range. The conventional ESR spectra indicate that the mobility of the spin labelled protein in the lipid gel phase decreases in the order: DMPG greater than DMPC/DMPG (1:1) greater than DMPC. In the liquid crystalline phase, the largest mobility is found in DMPC/DMPG (1:1, mol/mol) mixtures, but the mobility is still greater in DMPG than in DMPC. The results are interpreted in terms of different degrees of protein aggregation in the different lipids. Segmental motion with rotational correlation times on the order of tens of nanoseconds, motional anisotropy, and spectral overlap complicate the analysis of the STESR spectra. An estimate of the size of the protein aggregates is found to be in the region of 85 monomer units. Removing the polar tails from the protein by proteolytic digestion results in an enhanced aggregation in the gel phase. In the liquid crystalline phase, the segmental wobbling mobility of the protein is increased relative to the native protein, whereas the overall rotational diffusion is not changed greatly.

The three-dimensional structure of the bacterial virus MS2

The structure of the icosahedral bacteriophage MS2 has been determined to 3.3 A resolution by X-ray crystallography. The phase determination involved both molecular replacement at low resolution using a known structure and heavy-atom substitution. The coat protein has no structural similarity to that of any other known RNA virus.

Structure and function of conjugative pili: monoclonal antibodies as probes for structural variants of F pili

The lac-tra operon fusion plasmid pTG801 contains the known F plasmid DNA transfer (tra) genes required by Escherichia coli to elaborate functional F pili (T. Grossman and P. M. Silverman, J. Bacteriol. 171:650-656, 1989). Here, we show that these pili are actually structural variants of normal F pili and that the F plasmid must contain additional genes that affect pilus structure and function. We confirmed a previous report that two monoclonal antibodies that recognize epitopes at and near the amino terminus of F pilin do not decorate the sides of normal F pili, as determined by immunogold electron microscopy. However, both antibodies laterally decorated pTG801 pili. The epitope for one of the antibodies has been shown to include the amino-terminal acetyl group of F pilin, which must therefore also be present on pTG801 pilin. Normal antibody staining was restored to pTG801 pili when cells contained, in addition to pTG801, the compatible plasmid pRS31, which must therefore include at least one gene affecting F-pilus structure. One candidate, traD, was excluded as the sole such gene, since traD+ derivatives of a pTG801 strain still elaborated pili that could be laterally decorated with antibody. Moreover, although traD alone restored RNA bacteriophage R17 infectivity to pTG801 cells, as expected, it did not mimic pRS31 in restoring to pTG801 pili other characteristics of normal F pili. We conclude that pRS31 contains as yet uncharacterized genes required for elaboration of structurally normal F pili. Finally, we identified vesicular material, especially abundant in cultures of pTG801 transformants, that stained heavily with the anti-F-pilin monoclonal antibodies. This material may reflect the inner membrane pool of F pilin.

Conjugation system of IncC plasmid RA1, and the interaction of RA1 pili with specific RNA phage C-1

RA1 was the only IncC plasmid that was slightly temperature-sensitive for replication and transfer. At 30 degrees C, RA1 determined constitutive synthesis of conjugative pili and yet was transfer-repressed. Attachment of shaft-adsorbing RNA phage C-1 virions prevented the probable retraction of pili under heat stimulus (55 degrees C). Electron microscopy showed single adsorbed virions at pilus bases where they were thought to have stopped retraction.

Bacteriophage P1 tail-fibre and dar operons are expressed from homologous phage-specific late promoter sequences

Two plasmid systems, containing the easily assayable galK and lacZ functions, were employed to study the regulation of the bacteriophage P1 tail-fibre and dar operons. Various P1 DNA fragments carrying either the 5' end of lydA (the 1st gene in the dar operon) or the tail-fibre gene 19 precede the promoterless coding region of galK or were fused, in-frame, to the lacZ gene. In the presence of an induced P1 prophage, GalK and LacZ activities were both detected after a 20 to 30 minute lag period, indicating that the dar and tail-fibre operons are expressed from positively regulated, late promoters. The corresponding DNA operons are expressed from positively regulated, late promoters. The corresponding DNA region of the closely related p15B plasmid exhibits comparable promoter properties. Deletion analysis mapped the promoter of a gene 19-lacZ fusion to a DNA region upstream from gene R, an open reading frame that precedes the coding frame of gene 19. The tail-fibre gene thus forms the second gene in a three gene operon (genes R, 19 (S) and U). Sequence comparison between this promoter region, upstream sequences of the lydA gene and the corresponding portions of the p15B genome allowed the identification of a highly conserved 38 base-pair sequence, which most likely represents a P1-specific late promoter. This was confirmed by 5' mapping of P1 mRNA. Transcription of both the tail-fibre and dar operons is initiated at sites five and six base-pairs, respectively, downstream from the first conserved nucleotide of this sequence. The conserved motif consists of a standard Escherichia coli -10 region followed by a nine base-pair palindromic sequence located centrally about position -22.

Comparison of Vero-cytotoxin-encoding phages from Escherichia coli of human and bovine origin

Phages encoding production of Vero cytotoxins VT1 or VT2 were isolated from strains of Escherichia coli of human and bovine origin. Two human strains of serotype O157: H7 produced both VT1 and VT2 and each carried two separate phages encoding either VT1 or VT2. The phages were morphologically similar to each other and to a VT2 phage previously isolated from a strain of serotype O157: H-; all had regular hexagonal heads and short tails. The phages had similar genome sizes and DNA hybridization and restriction enzyme digestion showed that the DNAs were very closely related. This contrasts with another report that one of the strains tested (933) released two clearly distinguishable phages separately encoding VT1 and VT2. The O157 phages differed from a VT1 phage isolated from a bovine E. coli strain belonging to serotype O26: H11 and from the reference VT1 phage isolated previously from a human strain, H19, of serotype O26: H11. The two O26 phages were morphologically similar with elongated heads and long tails. They had similar genome sizes and DNA hybridization indicated a high level of homology between them. Hybridization of an O157 phage DNA probe to DNA of the O26 phages, and vice versa, showed there was some cross-hybridization between the two types of phage. A phage from a bovine strain of serotype O29: H34 had a regular hexagonal head and short tail resembling those of the O157 phages. The DNA was distinguishable from that of all the other phages tested in restriction digest patterns but hybridized significantly to that of an O157 phage. Hybridization of the phage genomes with VT1 and VT2 gene probes showed that sequences encoding these toxins were highly conserved in the different phages from strains belonging to the three serogroups.

Shiga-like toxin converting phage of enterohemorrhagic Escherichia coli strain 933

Production of Shiga-like toxin (SLT) by enterohemorrhagic Escherichia coli (EHEC) is controlled by phage conversion, and specific phages carry either the SLT-I or SLT-II operon. EHEC strain 933 produces both SLT-I and SLT-II. Previous studies demonstrated that the vast majority of phages recovered from strain 993 have hexagonal heads with short tails and encode SLT-II. However, conflicting results were obtained concerning the properties of SLT-I converting phages from strain 933. The present study reexamined the recovery of phages from 933 by various methods and characterized the restriction fragments from strain 933 DNA that hybridized with radiolabeled DNA from the SLT-I converting phage 933J, which has an elongated head with a long tail, and the SLT-II converting phage 933W. In the present study, only SLT-II converting phages like 933W were recovered from strain 933. A set of restriction fragments that hybridized with DNA from phage 933J but not 933W was present both in wild type strain 933 and in the variant 933D, which produces only SLT-I and was shown here to be cured of phage 933W. The sizes of the restriction fragments in strain 933 that were homologous with phage 933J differed, however, from those of phage 933J. These data indicate that the phage we isolated and named 933J probably did not originate from strain 933 as we originally reported. The present evidence demonstrates that strain 933 contains both the SLT-II converting phage 933W and other sequences of DNA homologous with phage 933J that probably represent a defective SLT-I converting phage.

Isolation and characterization of coliphage omega 18A specific for Escherichia coli O18ac strains

The bacteriophage omega 18A, specific for Escherichia coli O18ac strains, was isolated from sewage. The results of host range and conjugation experiments showed that the sensitivity of bacteria to the phage is associated with the presence of O18ac antigens. With some of the O18 strains the phage omega 18A produces clear lysis on bacterial lawns only when applied at a high multiplicity and moreover the phage does not multiply. With the help of the phage omega 18A, E. coli O18ac strains could be divided into two serologically distinct subgroups called O18A and O18A1. E. coli strains belonging to the subgroup O18A are sensitive to phage omega 18A whereas bacteria of subgroup A1 are resistant.

Structural responsiveness of filamentous bacteriophage Pf1: comparison of virion structure in fibers and solution. The effect of temperature and ionic strength

X-ray diffraction from fibers and magnetically oriented solutions has been used to study the effect of changes in environment on the helical symmetry and radial structure of the Pf1 virus particle. Detailed analysis of equatorial scattering to a spacing of 8-10 A was used to identify small radial motions of structural elements in the virus particle. R-factor ratios were used to determine the statistical significance of observed changes. Comparison of the structure of virus particles in fibers with those in solution indicated that the helical symmetry of the virions remains unchanged during fiber formation. In most fibers the virions appear to be slightly distorted by the tight packing of virus particles. This distortion results in an apparent increase in the radius of the virus particle of approximately 0.6 A. A change in the radius of the DNA is also observed. Increase in the concentration of solvent molecules during fiber formation results in penetration of the virus interior by some solvent components. NaCl is also able to enter the virus interior. The change in the helical symmetry of the virions at approximately 8 degrees C appears to be the same whether observed by diffraction from fibers or from solutions. Only subtle changes in radial structure are associated with the temperature transition.

Heterogeneity of Escherichia coli phages encoding Vero cytotoxins: comparison of cloned sequences determining VT1 and VT2 and development of specific gene probes

Phages coding for production of Vero cytotoxins VT1 or VT2 in strains of Escherichia coli serotype O157.H7 or O157.H- were morphologically indistinguishable. Their genome size and restriction enzyme digests of the phage DNA were similar. These phages were clearly different in these respects from a VT1-encoding phage isolated from a strain of E. coli O26.H11 (H19). However the VT1 region cloned from the phage originating in the E. coli O157.H7 strain was identical to the VT1 region previously cloned from the phage carried by H19. Sequences encoding VT2 that were cloned from the phage in E. coli O157.H- have been mapped and the VT2 region identified by transposon insertion. The cloned regions coding for VT1 or VT2 production had no similarities in the presence of restriction enzyme sites over a distance of about 2 kb, and two VT1-specific probes spanning a region of about 1.4 kb did not hybridize under stringent conditions with cloned VT2 DNA. A 2 kb HincII fragment contained the VT2 genes but hybridized to VT1-encoding phages and recombinant plasmids via flanking phage DNA. A 0.85 kb AvaI-PstI fragment was a specific probe for VT2 sequences and did not hybridize under stringent conditions to phages or plasmid recombinants encoding VT1.

Structure and dynamics of the Pf1 filamentous bacteriophage coat protein in micelles

The major coat protein of filamentous bacteriophage adopts its membrane-bound conformation in detergent micelles. High-resolution 1H and 15N NMR experiments are used to characterize the structure and dynamics of residues 30-40 in the hydrophobic midsection of Pf1 coat protein in sodium dodecyl sulfate micelles. Uniform and specific-site 15N labels enable the immobile backbone sites to be identified by their 1H/15N heteronuclear nuclear Overhauser effect and allow the assignment of 1H and 15N resonances. About one-third of the amide N-H protons in the protein undergo very slow exchange with solvent deuterons, which is indicative of sites in highly structured environments. The combination of results from 1H/15N heteronuclear correlation, 1H homonuclear correlation, and 1H homonuclear Overhauser effect experiments assigns the resonances to specific residues and demonstrates that residues 30-40 of the coat protein have a helical secondary structure.

Restoration of direct Fourier three-dimensional reconstructions of crystalline specimens by the method of convex projections

We consider the problem of the three-dimensional (3-D) reconstruction of objects by the direct Fourier method (DFM) and their restoration by the method of projections on to convex sets (POCS). The main discussion is centered on the case of specimens arranged in a two-dimensional (2-D) crystal and imaged by transmission electron microscopy, although the conclusions could be extended to more general cases. We present results of the restoration of the 3-D reconstruction of a computer generated 2-D crystal under different conditions of data collection limitation. A preliminary application with a real biological specimen (the connector of bacteriophage phi 29) is also presented. These results indicate that POCS can be used practically, in certain cases, to restore 3-D reconstructions obtained by the DFM, giving grounds for the proposal of the study of a combined DFM + POCS (reconstruction + restoration) method for the determination of biological structures by electron microscopy and 3-D image processing.

Characterization of phage 18, an unstable coliphage

Phage 18, a noninducible coliphage, is quite unstable and therefore difficult to study. Newly developed very gentle lysis and mounting techniques yielded isolated virions for examination by electron microscopy. The phage has a contractile tail with a length of 130 nm and an isometric head with a capsid diameter of 50 nm. Phage 18 is similar in morphology to phage P2 but is heteroimmune to it. DNA extracted from a clear-plaque mutant of phage 18 was subjected to BamHI restriction endonuclease digestion and was found to be easily distinguishable from the published restriction patterns for P2, phage 299, or phage 186 DNA. The genome size was calculated to be 33.5 kb. Using the DNA melting point, phage 18 DNA (G+C) content was determined to be 55.0% and its buoyant density was determined to be 1.715.