Filamentous bacterial viruses. II. Killing of bacteria by abortive infection with fd

Interaction between cyanophage MaMV-DC and eight Microcystis strains, revealed by genetic defense systems

Cyanophage MaMV-DC is a member of Myoviridae that was reported to specifically infect and lyse Microcystis aeruginosa FACHB-524 among 21 selected cyanobacterial strains. We reidentified the infection specificity of MaMV-DC among seven other Microcystis strains of different species. In our experiments, MaMV-DC infected three Microcystis strains but did not form plaque in Microcystis lawns. This indicated that MaMV-DC is at least a genus- rather than strain-specific virus. Cyanophage MaMV-DC genes were transcribed in M. aeruginosa FACHB-524, M. flos-aquae TF09, M. aeruginosa TA09 and M. wesenbergii DW09, and the growth of these Microcystis strains was inhibited by the addition of MaMV-DC. The predicted defense of eight Microcystis strains by CRISPR-Cas systems has shown mixed consistency with the infection experiment results, suggesting other defense or anti-defense systems play roles during infection process. Restriction-modification (RM) system analysis revealed an abundance of four types of RM proteins that may play roles in defense against cyanophages.

'Big things in small packages: the genetics of filamentous phage and effects on fitness of their host'

This review synthesizes recent and past observations on filamentous phages and describes how these phages contribute to host phentoypes. For example, the CTXφ phage of Vibrio cholerae encodes the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the emergence of new pathogenic strains. Other effects of filamentous phage include horizontal gene transfer, biofilm development, motility, metal resistance and the formation of host morphotypic variants, important for the biofilm stress resistance. These phages infect a wide range of Gram-negative bacteria, including deep-sea, pressure-adapted bacteria. Many filamentous phages integrate into the host genome as prophage. In some cases, filamentous phages encode their own integrase genes to facilitate this process, while others rely on host-encoded genes. These differences are mediated by different sets of 'core' and 'accessory' genes, with the latter group accounting for some of the mechanisms that alter the host behaviours in unique ways. It is increasingly clear that despite their relatively small genomes, these phages exert signficant influence on their hosts and ultimately alter the fitness and other behaviours of their hosts.

Bacteriophage and phenotypic variation in Pseudomonas aeruginosa biofilm development

A current question in biofilm research is whether biofilm-specific genetic processes can lead to differentiation in physiology and function among biofilm cells. In Pseudomonas aeruginosa, phenotypic variants which exhibit a small-colony phenotype on agar media and a markedly accelerated pattern of biofilm development compared to that of the parental strain are often isolated from biofilms. We grew P. aeruginosa biofilms in glass flow cell reactors and observed that the emergence of small-colony variants (SCVs) in the effluent runoff from the biofilms correlated with the emergence of plaque-forming Pf1-like filamentous phage (designated Pf4) from the biofilm. Because several recent studies have shown that bacteriophage genes are among the most highly upregulated groups of genes during biofilm development, we investigated whether Pf4 plays a role in SCV formation during P. aeruginosa biofilm development. We carried out immunoelectron microscopy using anti-Pf4 antibodies and observed that SCV cells, but not parental-type cells, exhibited high densities of Pf4 filaments on the cell surface and that these filaments were often tightly interwoven into complex latticeworks surrounding the cells. Moreover, infection of P. aeruginosa planktonic cultures with Pf4 caused the emergence of SCVs within the culture. These SCVs exhibited enhanced attachment, accelerated biofilm development, and large regions of dead and lysed cells inside microcolonies in a manner identical to that of SCVs obtained from biofilms. We concluded that Pf4 can mediate phenotypic variation in P. aeruginosa biofilms. We also performed partial sequencing and analysis of the Pf4 replicative form and identified a number of open reading frames not previously recognized in the genome of P. aeruginosa, including a putative postsegregational killing operon.

High-frequency interconversion of turbid and clear plaque strains of bacteriophage f1 and associated host cell death

Under normal cultivation conditions, a mixture of turbid and clear plaques is often apparent in cultures of bacterial cells infected with filamentous bacteriophages. Beginning with a culture of wild-type filamentous phage f1, which itself produces turbid plaques, a clear plaque strain (c1) was isolated. From c1, the turbid plaque strain t1 was isolated; from t1, the clear plaque strain c2 was isolated; and from c2, the turbid plaque strain t2 was isolated. Each of these strains was generated with a frequency of approximately 1 × 10-4. Although filamentous phages have been thought not to induce host cell death, both turbid and clear plaque strains of f1 killed host bacteria. Plating of bacterial cells 1 h after infection revealed that colonies produced by cells infected with either wild-type f1 or strain c2 were smaller than those derived from uninfected cells, and that colony formation by infected cells was reduced by 15% and 38%, respectively. The time course of bacterial growth revealed that, at 4 h after infection, the number of CFU per milliliter of culture of cells infected with wild-type f1 or with strain c2 was reduced by 27% and 95%, respectively, compared with that for uninfected cells. Microculture analysis also revealed that the percentages of nondividing cells in f1 or c2 infected were 19% and 52%, respectively, 4 h after infection with wild-type f1 or with strain c2; no such cells were detected in cultures of uninfected cells. Negative staining and electron microscopy showed that 20% and 61% of cells infected with wild-type f1 or with strain c2 were dead 4 h postinfection. Finally, although the rates of DNA synthesis were similar for infected and uninfected cells, the rates of RNA and protein synthesis were markedly reduced in infected cells.Key words: Escherichia coli, bacteriophages, turbid plaque, clear plaque.

Roles of pIII in filamentous phage assembly

Filamentous phage protein III (pIII), located at one end of the phage, is required for infectivity and stability of the particle. Cells infected with phage from which gene III has been completely deleted produce particles that are not released into the medium but stay associated at the surface. These particles are much longer than normal phage. They can be released by subsequent expression of pIII. Viewed with the electron microscope, cells infected with gene III deletion phage are decorated with structures that resemble extremely long pili. Surprisingly, such cells are viable and can form colonies. The pIII deficiency can be complemented in trans, but there is a threshold concentration below which assembly does not occur. Above this threshold, pIII is used very efficiently and is incorporated into infectious but longer than unit length phage. As the concentration of pIII is increased, the number of infectious particles increases, and their average length decreases.pIII stabilizes pVI, a second phage protein found at the pIII end of the particle. In the absence of pIII, degradation of pVI is very rapid. pIII is thus not only required for infectivity and particle stability, but to terminate assembly and release the phage from its assembly site.

A long lytic cycle in filamentous phage Cf1tv infecting Xanthomonas campestris pv. citri

In this study the lytic cycle of a filamentous phage is reported. Under normal laboratory cultivation conditions a virulent form could spontaneously and easily arise from a temperate phage. The virulent one could superinfect cells containing Cf1t lysogen. Therefore, we have named it Cf1tv. In a colony formation assay using cells from an infected culture, two types of colonies were observed, small and large. It could be proven that the formation of small colonies is the result of killing during Cf1tv infection. The number of small colony forming units (cfu) increased with infection time and reached a maximum at 16 h after infection, then dropped to the initial cell concentration at 28 h after infection; 28 h were required to kill all infected cells. Large colonies contained uninfected or phage-resistant cells, but no lysogenic cells. Bacterial death was further confirmed by a microculture assay. At 2 h after infection, normal-dividing cells (cfu giving large colonies) contained about 40% of Cf1tv-infected cells, then the percentage decreased with infection time. Slow-dividing cells (infected cfu giving small colonies) initially contained 55% of cells; this percentage increased slightly at 4 h after infection, then decreased at 8 h after infection. Non-dividing cells initially contained 5% of infected cells, then their numbers rapidly increased with time after infection. The cell division was seriously affected and finally stopped. During one-step growth, the latent period was 30 min and there was no burst; phages were released at 30 min after infection and the rate of release increased gradually with time after infection. Phage DNA integration into host chromosome could not be observed.

Filamentous phages as cloning vectors

The virtue of Ff vectors goes beyond the fact that they deliver a single strand in a convenient package for sequencing and oligonucleotide-directed mutagenesis. Of all vectors in common use they are the easiest to propagate and process. Their genomes can be easily manipulated, and the knowledge acquired over a quarter century of basic research makes their behavior reasonably predictable. For this reason I have emphasized the general properties of Ff phage in this review and dealt at some length with applications that are still not fully developed, I hope this review will inspire readers to continue the tradition of imaginative exploitation of this unique class of viruses.

Cloning and expression of the filamentous bacteriophage Pf1 major coat protein gene in Escherichia coli. Membrane protein processing and virus assembly

A restriction fragment carrying the major coat protein gene (gene VIII) was excised from the replicative form (RF) DNA of the class II filamentous bacteriophage Pf1, which infects Pseudomonas aeruginosa. This fragment was cloned into the expression plasmid pKK223-3, where it came under the control of the tac promoter. In transformed Escherichia coli JM101 cells, in the presence of the inducer isopropyl-beta-D-thiogalactoside, the bacteriophage Pf1 gene was strongly expressed. The bacteriophage Pf1 coat protein displays the same pattern of negatively charged N-terminal region, hydrophobic middle region and positively charged C-terminal region as that of its counterpart in the class I bacteriophage fd, which infects E. coli, but otherwise the two proteins have no sequence homology. However, the Pf1 procoat protein was found to undergo processing and insertion into the E. coli cell inner membrane, like its fd counterpart, demonstrating that this part of the assembly process is the same for these different bacteriophages. The complete transcriptional unit, incorporating the tac promoter and rrnB transcription terminators flanking the Pf1 coat protein gene, was excised from the expression plasmid and cloned into the intergenic space of bacteriophage R252, an fd bacteriophage that carries an amber mutation in its own major coat protein gene. The Pf1 coat protein gene was again well expressed in infected E. coli cells but the chimeric bacteriophage had growth properties identical to those of the parent bacteriophage R252 on suppressor and non-suppressor strains of E. coli. The class I bacteriophage Pf1 coat protein evidently cannot be recognized by the class I bacteriophage assembly complex at or in the E. coli cell inner membrane, either at the point of initiation of assembly or during the elongation process.

Gene-III protein of filamentous phages: evidence for a carboxyl-terminal domain with a role in morphogenesis

A filamentous phage derivative, fCA55, bearing a nonpolar deletion in gene III, has been constructed and characterized to study the functions of that gene. The deletion eliminates most of gene III without disturbing its reading frame or the putative promoter for the downstream gene, VI. Therefore it is assumed that any abnormalities exhibited by fCA55 are a direct effect of the gene-III lesion itself, and not polar effects on other genes. fCA55 Is abnormal in two respects. First, it is noninfective; in this it resembles another nonpolar gene-III deletion mutant, fKN16, which is missing 507 bp encompassing roughly the first half of the gene. Second, it is secreted as polyphage--very long particles containing many unit-length DNA molecules; in this respect, fCA55 differs from fKN16. When the viral proteins of these two mutants were analyzed with antibody directed against gene-III protein, it was found that fKN16 contains an altered gene-III protein, while fCA55 is unreactive. It was concluded that the gene-III protein has two functional domains: the N-terminal domain, missing in both mutants, is required for viral infectivity; while the C-terminal domain, partly missing in fCA55 but retained in fKN16, is incorporated into the virion, and is responsible for the protein's role in generating normal, unit-length particles.

A bacterial gene, fip, required for filamentous bacteriophage fl assembly

An Escherichia coli mutant which does not support the growth of filamentous bacteriophage fl allows phage fl DNA synthesis and gene expression in mutant cells, but progeny particles are not assembled. The mutant cells have no other obvious phenotype. On the basis of experiments with phage containing nonlethal gene I mutations and with mutant fl selected for the ability to grow on mutant bacteria, we propose an interaction between the morphogenetic function encoded by gene I of the phage and the bacterial function altered in this mutant. The bacterial mutation defines a new gene, fip (for filamentous phage production), located near 84.2 min on the E coli chromosome.

A mutation downstream from the signal peptidase cleavage site affects cleavage but not membrane insertion of phage coat protein

Morphogenesis of filamentous phage includes synthesis of the phage major coat protein in precursor form, its insertion into the host cell plasma membrane, its cleavage to the mature form of the protein, and its assembly there into virions. The M13 mutant am8H1R6 encodes a coat protein in which leucine replaces glutamic acid as residue 2 of the mature protein [Boeke, J. D., Russel, M. & Model, P. (1980) J. Mol. Biol. 144, 103-116]. The coat protein precursor produced by this variant is a poor substrate for the Escherichia coli signal peptidase both in vivo and in vitro. This pre-coat protein, which is eventually processed and assembled into viable phage particles, is associated with the membrane fraction of the infected cell. We conclude that the domain recognized by the signal peptidase extends beyond the signal peptide itself. Furthermore, membrane association and signal peptide cleavage can be separated temporally under conditions that permit membrane insertion, cleavage, and phage assembly.

Segregation into the replication of bacteriophage M 13 DNA in minicells of Escherichia coli

Minicells derived from E. coli x796(F+) are refractory to infection by phage M 13. However, after infection of the minicell-producing strain with M 13, phage DNA is found to segregate efficiently into newly formed minicells. The M 13 specific DNA present in minicells isolated several hours after infection consists of single stranded viral DNA and double stranded replicative forms in nearly equal amounts. M 13 DNA containing minicells are capable of carrying out at least one complete round of single stranded DNA synthesis as shown by the flow of label from replicative forms to free single strands.

Filamentous bacterial viruses. V. Asymmetric replication of fd duplex deoxyribonucleic acid

Short pulses (30 sec at 32 C) of (3)H-thymidine were found primarily in the viral strands of replicating fd deoxyribonucleic acid (DNA), even at a time when most DNA being synthesized was duplex DNA. Much of the labeled viral strand DNA was longer than unit length, but some was shorter than unit length. Most of the corresponding complementary-strand DNA was recovered in closed supercoiled duplex molecules, even for short pulses; the remainder of the complementary-strand DNA was found in replicative intermediates in pieces shorter than unit length. Some of the viral strands in open replicating DNA lacked a corresponding complementary strand.