Bacteriophage F1 Research Articles

A vector for the construction of translational fusions to TEM β-lactamase and the analysis of protein export signals and membrane protein topology

A plasmid vector, pJBS633, that facilitates the construction of translational fusions of genes of interest to the coding region of the mature form of TEM β-lactamase has been developed. Transformants containing in-frame fusions can be identified by their ability to grow when plated at high inocula on agar containing ampicillin (Ap). The cellular location of the β-lactamase moiety of the fusion proteins can then be determined since only those that direct the translocation of the β-lactamase across the cytoplasmic membrane to the periplasm result in the ability of individual cells of Escherichia coli to form isolated colonies in the presence of Ap. Conversely, those fusion proteins in which the β-lactamase moiety remains cytoplasmic do not protect individual cells against Ap. Transformants expressing the latter class of fusion proteins can, however, be identified when plated at high inocula since, as cells start to lyse, the cytoplasmic β-lactamase activity is released and provides Ap resistance to the surrounding cells. The vector contains the origin of replication of f1 phage so that single-stranded plasmid DNA can be obtained in the appropriate orientation to allow sequencing across the fusion junction using a universal primer complementary to the start of the coding region of mature TEM β-lactamase. pJBS633 should be useful as a general vector for the construction of β-lactamase fusions and, in particular, for the analysis of protein export signals and the determination of the organisation of proteins in the E. coli cytoplasmic membrane.

Concentration of Viruses from Water using Pig Erythrocyte Ghost Cells

Ghost cells (made from pig erythrocytes) were used as a sorptive matrix to concentrate bacteriophages ϕx-174, MS-2, f2, and Poliovirus LSC-l strain from small volumes of water. Adsorption-elution process was similar to the organic flocculation method, (adsorption performed at pH 3.5) but instead of beef-extract floc, erythrocyte membranes were used. The adsorption achieved ranged 93-100% with various bacteriophages and 97-100% with Poliovirus LSC-1 strain, elution ranged 92-102% with bacteriophages and 84-347% with the Poliovirus. Comparing ghost cell results with 3% beef-extract from different sources, the pig erythrocyte ghost cells were always found to be superior.

Assembly site of bacteriophage f1 corresponds to adhesion zones between the inner and outer membranes of the host cell.

Morphogenesis of the filamentous bacteriophage f1 occurred at adhesion zones between the inner and outer membranes of the host cell. Quantitation of adhesion zones in cells infected with mutant phage strains suggested that the phage gene I protein may be involved in the formation of adhesion zones for phage assembly.

FipB and fipC: two bacterial loci required for morphogenesis of the filamentous bacteriophage f1.

We describe the identification of two mutations in bacterial genes, designated as fipB and fipC, which resulted in temperature-sensitive morphogenesis of bacteriophage f1. These mutations mapped at separate loci but had to be present simultaneously to block f1 production at 41.5 degrees C. One mutation defined the locus fipB at 85.3 min on the Escherichia coli linkage map; the other defined the locus fipC, which mapped very close to rpsL at 73 min. Since these mutations did not appear to affect phage DNA replication, gene expression, or protein localization, they probably interfered with the its life cycle at the level of assembly. fipB mutants were partially deficient in adsorption of bacteriophage lambda, and fipB and fipC mutants leaked beta-lactamase into the medium, suggesting that the mutations affect outer-membrane structure or function.

Inactivation of Norwalk virus in drinking water by chlorine.

Norwalk virus in water was found to be more resistant to chlorine inactivation than poliovirus type 1 (LSc2Ab), human rotavirus (Wa), simian rotavirus (SA11), or f2 bacteriophage. A 3.75 mg/liter dose of chlorine was found to be effective against other viruses but failed to inactivate Norwalk virus. The Norwalk virus inoculum remained infectious for five of eight volunteers, despite the initial presence of free residual chlorine. Infectivity in volunteers was demonstrated by seroconversion to Norwalk virus. Fourteen of 16 subjects receiving untreated inoculum seroconverted to Norwalk virus. Illness was produced in four of the eight volunteers and in 11 of 16 control subjects. A similar Norwalk virus inoculum treated with a 10 mg/liter dose of chlorine produced illness in only one and failed to induce seroconversion in any of eight volunteers. Free chlorine (5 to 6 mg/liter) was measured in the reaction vessel after a 30-minute contact period. Norwalk virus appears to be very resistant to chlorine which may explain its importance in outbreaks of waterborne disease.

Direct cloning of the trxB gene that encodes thioredoxin reductase.

A strain was constructed which contains mutations in the genes encoding thioredoxin (trxA) and thioredoxin reductase (trxB) such that filamentous phage f1 cannot grow. The complementation of either mutation with its wild-type allele permits phage growth. We used this strain to select f1 phage which contain a cloned trxB gene. The location of the gene on the cloned fragment was determined, and its protein product was identified. Plasmid subclones that contain this gene overproduce thioredoxin reductase.

Thioredoxin is the bacterial protein encoded by fip that is required for filamentous bacteriophage f1 assembly.

Escherichia coli mutants defective in the fip gene contain reduced levels of thioredoxin activity. F' derivatives of trxA mutants failed to support f1 growth, although suppressors of an amber trxA mutation restored both thioredoxin activity and the Fip+ phenotype. Plasmids carrying the trxA gene restored the Fip+ phenotype to fip strains.

Nucleotide sequence and genetic organization of the genome of the N-specific filamentous bacteriophage IKe: Comparison with the genome of the F-specific filamentous phages M13, fd and f1

The nucleotide sequence and genetic organization of the genome of the N-specific filamentous single-stranded DNA phage IKe has been established and compared with that of the F-specific filamentous phages M13, fd and f1 (Ff). The IKe DNA sequence comprises 6883 nucleotides, which is 476 (475) nucleotides more than the nucleotide sequence of the Ff genome. The data indicate that IKe and Ff have evolved from a common ancestor (overall homology approx. 55%) and that their genomes contain ten homologous genes, the order of which is identical. Similar to Ff, the major coat protein and the gene III-encoded pilot protein of IKe are synthesized via precursor molecules. The extent of homology between the genes of IKe and Ff differs significantly from one gene to another. Genes that code for viral capsid proteins are less homologous than genes whose products are involved in the processes of DNA replication and phage morphogenesis. During evolution, large nucleotide sequence rearrangements have occurred in the gene (gene III) whose product is needed for the attachment of the virion to the conjugative pili of the host cell, suggesting that these rearrangements have led to phages with different host specificities. Extensive nucleotide sequence homology was noted between the structural elements involved in DNA replication and phage morphogenesis, indicating that the mechanisms involved in DNA replication and morphogenesis are highly conserved.

Plasmid pFCE4: A new system of Escherichia coli expression-modification vectors

Two versatile expression-modification vectors were obtained by inserting the origin of replication ( ori) of phage f1 into the expression vector pOTS. The resulting plasmids produce large amounts of coding or noncoding ssDNA (depending on ori orientation in pFCE4 + and pFCE4 −) and excrete it into the medium as virus-like particles following infection with phage f1. These features make them suitable for dideoxy chain termination sequencing, oligonucleotide directed mutagenesis and gene expression without further manipulations. The human IFN α-2 gene, lacking the codon for the first amino acid, cysteine, was efficiently expressed by these vectors.

Fine structure of a membrane anchor domain

We describe a detailed deletion analysis of the anchoring domain of a model membrane protein. Removal of the 23 contiguous uncharged amino acids from the carboxy terminus of the bacteriophage f1 gene III protein (pIII) converts it from an integral membrane protein to a secreted periplasmic form. Deletions that remove six or fewer residues of the hydrophobic core result in no diminution of the protein's capacity to anchor in the membrane. Longer deletions into this hydrophobic domain gradually destabilize the protein-membrane association. pIII derivatives with over half of the hydrophobic core deleted retain substantial residual anchor function. The basic residues, arginine and lysine, which provide a carboxy-terminal boundary for this domain, can be deleted without loss of anchoring capacity.

Single stranded DNA SP6 promoter plasmids for engineering mutant RNAs and proteins: synthesis of a 'stretched' preproparathyroid hormone.

The intergenic region of bacteriophage f1 has been subcloned into the bacteriophage SP6 promoter plasmids, pSP64 and pSP65, in both orientations. Coinfection of E. coli with these SP6 promoter/phage f1 chimeric plasmids and the interference resistance phage, IR1, results in the replication and secretion of the pSP6.f1 plasmids as single stranded DNA. Bovine preProPTH cDNAs in both the native form and a form containing an insertion of 117 base pairs in the protein coding region have been inserted in these plasmids. The RNA transcribed from the SP6.f1/preProPTH cDNA constructs was efficiently translated in the wheat germ or reticulocyte cell free systems without addition of a 7-methylguanosine cap to the RNA. In the presence of dog pancreatic or chicken oviduct microsomal membranes, conversion of the resultant pre-proteins to pro-proteins was observed. Confirmation of the "mutated" preProPTH cDNA was determined by dideoxyribonucleotide DNA sequencing of single stranded plasmid DNA. These vectors are suitable for the efficient biosynthesis of large amounts of single or double stranded DNA, and translationally active RNA. The combined properties of single stranded DNA replication and the SP6 promoter simplify the engineering of mutant RNAs and their corresponding proteins. In addition, single stranded DNA or RNA corresponding to either complementary strand may be synthesized as nucleic acid hybridization probes.

Vectors for the direct selection of cDNA clones corresponding to mammalian cell mRNA of low abundance

We have constructed two cDNA cloning vectors which (1) carry the intergenic region of phage f1 and (2) permit efficient cloning (by the Okayama-Berg procedure) of full-length copies of mammalian mRNA in either orientation. Infection of cells harboring these vectors with f1 phage results in the encapsidation of single-stranded (ss) plasmid DNA carrying either the sense or the anti-sense sequence of the cDNA inserts. The complementary nature of the cDNA inserts in two such cDNA libraries facilitates preparative hybridization procedures. These vectors have general applicability to any eukaryotic system where changes in the abundance of mRNA transcripts are to be measured and the corresponding cDNA clones isolated.

Plasmids pEMBLY: new single-stranded shuttle vectors for the recovery and analysis of yeast DNA sequences

We describe the construction and properties of pEMBLY plasmids. They belong to a new family of yeast shuttle vectors which are derived from plasmid vector pEMBL9 and offer the following improvement: (i) relatively small size; (ii) large number of cloning sites; (iii) screening for insert-containing plasmids on indicator plates; (iv) different combinations of genes which complement auxotrophic deficiencies and sequences that support DNA replication in Saccharomyces cerevisiae; and (v) ability to isolate the plasmid DNA in single-stranded (ss) form. The yeast S. cerevisiae can be efficiently transformed by these plasmids in both the ss and double-stranded (ds) forms. Finally, the presence of the phage f1 intergenic region allows one to obtain the cloned sequences in the ss form upon infection with the wild-type ss phage [Dotto et al., Virology 114 (1981) 463–473].

Gene X of bacteriophage f1 is required for phage DNA synthesis: Mutagenesis of in-frame overlapping genes

The gene II protein of bacteriophage f1 is a site-specific endonuclease required for initiation of phage viral strand DNA synthesis. Within gene II is another gene, X, encoding a protein of unknown function identical to the C-terminal 27% of the gene II protein, and separately translated from codon 300 (AUG) of gene II. By oligonucleotide mutagenesis, we constructed phage mutants in which this codon has been changed to UAG (amber) or UUG (leucine), and propagated them on cells carrying a cloned copy of gene X on a plasmid. The amber mutant makes no gene X protein, and cannot grow in the absence of the complementing plasmid; the leucine-inserting mutant can make gene X protein, and grows normally without the plasmid. Without gene X protein, phage DNA synthesis (particularly viral strand synthesis) is impaired. We discuss this finding in the context of other known in-frame overlapping genes (particularly genes A and A ∗ of phage φX174), many of which are also involved in the specific initiation of DNA synthesis, and suggest applications for the mutagenic strategy we employed.

Transcription in bacteriophage f1-infected Escherichia coli: RNA synthesized on DNA of deletion mutant PII shows the existence of a two-site terminator.

Two different transcripts are synthesized on the DNA of deletion mutant PII of bacteriophage f1 in E. coli cells infected with this miniphage. Both RNA species appear to be primary transcripts and differ by about 100 nucleotides at their 3'OH end. Mapping of these molecules on the miniphage genome suggests that a two-site terminator is active at the end of the I region of transcription of bacteriophage f1.

Inactivation of enteroviruses, rotaviruses and bacteriophages by peracetic acid in a municipal sewage effluent

The virucidal efficacy of peracetic acid (PAA) was evaluated against poliovirus 1, echovirus 1, coxsackievirus B5, human rotavirus, simian rotavirus SA11 and bacteriophage f2 in a municipal sewage effluent. The results indicated relatively high concentrations of acid were required to achieve significant inactivation. Human rotavirus, which was the most resistant, required 140 ppm to achieve 99.99% inactivation. On the other hand, simian rotavirus SA11, which was the most sensitive, required only 20 ppm to achieve the same degree of inactivation. The three enteroviruses reacted similarly and the bacteriophage was slightly less resistant than the enteroviruses, especially at high concentrations of peracetic acid. The effluent did not exert a demand for peracetic acid. Temperature, organic matter and suspended solids had negligible effects on the virucidal efficacy of peracetic acid.

Ghost cells as sorption matrix for virus concentration from water.

Pig erythrocyte membranes were used as adsorbent material for the concentration of bacteriophage phi x-174, MS-2, and f2 from 5 ml of saline solution. The adsorption was carried out at pH 3.5, and the elution was carried out at pH 7.0. Compared with adsorption on 3% beef extract, bacteriophage adsorption on erythrocyte ghost cells yielded 93 to 100%, and elution was 92 to 100%, whereas beef extract organic flocculation yielded adsorption of 0 to 98.8% and elution of 61 to 86.6%. The same procedure but with poliovirus LSC-1 gave 100% adsorption and 91 to 129% elution.

Rho-dependence of the terminator active at the end of the I region of transcription of bacteriophage f1.

Infection of rho- Escherichia coli cells with deletion mutant PII of bacteriophage f1 results in a miniphage RNA population composed of transcripts longer than those synthesized in the infection of rho+ cells. This indicates a Rho dependence of the terminator active at the end of the I region of transcription of bacteriophage f1. An estimate of the length of a transcript, which represents a good fraction of the RNA that passes beyond the terminator, indicates that the hairpin structure where synthesis of complementary strand DNA initiates also acts as a fairly efficient Rho-independent terminator.

Enzymatic techniques for the isolation of random single-base substitutions in vitro at high frequency.

A general and efficient method has been developed to generate large numbers of single-base substitution mutations simply and rapidly. A unique f1 phage recombinant DNA cloning vector is described, which contains the phi X174 origin of viral strand DNA synthesis and allows one to direct mutagenesis to any specific segment of DNA. Gapped circular DNA is constructed by annealing viral single-stranded circular DNA [ss(c) DNA] with a mixture of linear duplex DNAs that have had their 3'-OH termini processively digested with Escherichia coli exonuclease III under conditions in which the resulting, newly generated 3'-OH termini present in the various hybrid molecules span the region of interest. Base changes are induced by misincorporation of an alpha-thiodeoxynucleoside triphosphate analog onto this primer-template, followed by DNA repair synthesis. The asymmetric segregation of mutants from wild-type sequences is accomplished by double-stranded replicative form DNA----ss(c) DNA synthesis in vitro, initiated from the phi X174 viral strand origin sequence present on the vector DNA. Mutated ss(c) DNA is screened by the dideoxy chain termination method. In one mutagenesis experiment, 21 independent single-base substitutions were isolated in a 72-nucleotide-long target region. DNA sequence analysis showed that all possible base transversions and transitions were represented.

Minor protein content of the gene V protein/phage single-stranded DNA complex of the filamentous bacteriophage f1

The gene V protein/phage single-stranded (SS) DNA complex is an intermediate in the assembly of the filamentous bacteriophage f1. The minor protein content of this complex isolated from wild-type and amber mutant phage-infected Escherichia coli bacteria has been analyzed. Other than the gene V protein, none of the proteins found in purified samples of the complex correspond to any known phage gene products. In particular, the minor coat proteins found in the mature phage particle do not appear to be components of the cytoplasmic gene V protein/f1 SS DNA complex. However, approximately 1–3 molecules of E. coli single-stranded DNA binding protein (SSB) copurify with the complex and may be stably associated with this structure in vivo.