Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages

Marine cyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant photosynthetic organisms on earth, spanning vast regions of the oceans and contributing significantly to global primary production. Their viruses (cyanophages) greatly influence cyanobacterial ecology and evolution. Although many cyanophage genomes have been sequenced, insight into the functional role of cyanophage genes is limited by the lack of a cyanophage genetic engineering system. Here, we describe a simple, generalizable method for genetic engineering of cyanophages from multiple families, that we named REEP for REcombination, Enrichment and PCR screening. This method enables direct investigation of key cyanophage genes, and its simplicity makes it adaptable to other ecologically relevant host-virus systems. T7-like cyanophages often carry integrase genes and attachment sites, yet exhibit lytic infection dynamics. Here, using REEP, we investigated their ability to integrate and maintain a lysogenic life cycle. We found that these cyanophages integrate into the host genome and that the integrase and attachment site are required for integration. However, stable lysogens did not form. The frequency of integration was found to be low in both lab cultures and the oceans. These findings suggest that T7-like cyanophage integration is transient and is not part of a classical lysogenic cycle.Subject terms: Microbial ecology, Bacteriophages     

OCCURRENCE OF A TEMPERATE CYANOPHAGE LYSOGENIZING THE MARINE CYANOPHYTE PHORMIDIUM PERSICINUM1

A temperate cyanophage was found to lysogenize the marine cyanophyte Phormidium persicinum (Reinke) Com. (Provasoli strain). The lytic cycle was induced by the addition of mitomycin C or by brief illumination with ultraviolet light. The lytic process observed under the electron microscope showed that phage particles appeared in a nucleoplasm region 15 to 24 h after the addition of mitomycin C. The induction of the lytic process occurred simultaneously in almost all cells of every trichome. Matured phage particles were released to the medium 30 to 50 h after the addition of mitomycin C. Phage particles isolated from algal lysates had a polyhedral head (about 40 nm in diameter) with a long (about 300 nm) and noncontractile tail. The most abundant protein, presumably a structural protein, had an apparent molecular mass of about 38 kDa. The genome size estimated from restriction analysis was about 50 kbp. Phage DNA was digested with several restriction endonucleases including Sau3AI and DpnI. However, MboI failed to digest the phage DNA, suggesting that the phage DNA is highly methylated. Southern blot analysis suggested that some part of the phage was in the lytic cycle in algal cells growing under normal conditions. A possible role of temperate cyanophages in the regulation of cyanophyte populations in the marine environment is discussed.     

AS-1L - a newly discovered strain of Cyanophage AS-1 in GDR

In samples, taken from waters in the surroundings of Leipzig (GDR) in 1978, we found cyanophages in Central Europe for the first time. Among other cyanophages we isolated the new strain AS-1L. Out of 20 tested cultures of unicellular cyanobacteria seven strains belonging to the genus Synechococcus proved to be susceptible for this cyanophage. In morphology AS-1L corresponds to the cyanophage AS-1 found in the U.S.A., to which it is related serologically, too. AS-1L differs from the other strains of AS-1 by a shorter growth cycle, especially a shorter latent period, by the kinetics of inactivation by antiserum, and by a somewhat narrower pH scope of stability. Consequently the isolated cyanophage is to be looked at as a new strain of the cyanophage AS-1.     

Isolation and characterization of a novel Lambda-like phage infecting the bloom-forming cyanobacteria Cylindrospermopsis raciborskii

Cylindrospermopsis raciborskii is a central bloom-forming cyanobacteria. However, despite its ecological significance, little is known of its interactions with the phages that infect it. Currently, only a single sequenced genome of a Cylindrospermopsis-infecting phage is publicly available. Here we describe the isolation and characterization of Cr-LKS3, a second phage infecting Cylindrospermopsis. Cr-LKS3 is a siphovirus with a higher genome similarity to prophages within heterotrophic bacteria genomes than to any other cyanophage/cyano-prophage, suggesting that it represents a novel cyanophage group. The function, order and orientation of the 72 genes in the Cr-LKS3 genome are highly similar to those of Escherichia virus Lambda (hereafter Lambda), despite the very low sequence similarity between these phages, showing high evolutionary convergence despite the substantial difference in host characteristics. Similarly to Lambda, the genome of Cr-LKS3 contains various genes that are known to be central to lysogeny, suggesting it can enter a lysogenic cycle. Cr-LKS3 has a unique ability to infect a host with a dramatically different GC content, without carrying any tRNA genes to compensate for this difference. This ability, together with its potential lysogenic lifestyle shed light on the complex interactions between C. raciborskii and its phages.     

Effects of photosynthetic inhibitors and light-dark regimes on the replication of cyanophage SM-2

The effects of photosynthetic inhibitors and light-dark regimes on the replication of cyanophage SM-2 in its host cyanobacteria (Synechococcus elongatus UTEX 563 and Microcystis aeruginosa NRC-1, Synechococcus NRC-1 UTEX 1937) have been investigated. Photoassimilation of CO₂ by infected cells was enhanced and remained elevated until late in the infection cycle. Photosynthetic inhibitors and the removal of light suppressed viral replication. SM-2, like other cyanophage of unicellular cyanobacteria, is highly dependent on host photosynthetic metabolism for the energy required in replication.Abbreviations DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - CCCP carbonyl-cyanide m-chlorophenyl hydrazone - MMH Modified Modified Hughes Medium     

Effect of some environmental factors on cyanophage AS-1 development in Anacystis nidulans

The development cycle of the cyanophage AS-1 was studied in the host blue-green alga, Anacystis nidulans, under conditions that impair photosynthesis and under various light/dark regimes. Under standard conditions of incubation the 16-h development cycle consisted of a 5-h eclipse period and an 8-h latent period. Burst size was decreased by dark incubation to 2% of that observed in the light. An inhibitor of photosystem II, 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU), reduced the burst size to 27% of that of the uninhibited control, whereas cyanophage production was completely abolished by carbonyl-cyanide m-chlorophenyl hydrazone (CCCP), an inhibitor of photosynthetic electron transport. Dark incubation of infected cells decreased the latent period by 1–2 h and the eclipse period by 1 h, once the cultures were illuminated. This suggests that adsorption took place in the dark. Intracellular growth curves indicated that light is necessary for viral development. Infected cells must be illuminated at least 13 h to produce a complete burst at the same rate as the continuously illuminated control. Low light intensities retarded the development cycle, and at lowest light intensities no phage yield was obtained. AS-1 is highly dependent on host cell photophosphorylation for its development.List of Abbreviations CCCP Carbonyl-cyanide m-chlorophenyl hydrazone - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethyl urea - m.o.i. multiplicity of infection - O.D. optical density - PFU plaque-forming unit Dedicated to Prof. Roger Y. Stanier on the occasion of his 60th birthday     

Genomic Sequence and Evolution of Marine Cyanophage P60: a New Insight on Lytic and Lysogenic Phages

The genome of cyanophage P60, a lytic virus which infects marine Synechococcus WH7803, was completely sequenced. The P60 genome contained 47,872 bp with 80 potential open reading frames that were mostly similar to the genes found in lytic phages like T7, phi-YeO3-12, and SIO1. The DNA replication system, consisting of primase-helicase and DNA polymerase, appeared to be more conserved in podoviruses than in siphoviruses and myoviruses, suggesting that DNA replication genes could be the critical elements for lytic phages. Strikingly high sequence similarities in the regions coding for nucleotide metabolism were found between cyanophage P60 and marine unicellular cyanobacteria.     

Isolation and characterization of a temperate cyanophage for a tropical Anabaena strain

In this paper we describe the isolation and characterization of a temperate cyanophage N(S)1 of the genus cyanopodovirus which produces turbid plaques on the host Anabaena 77S15 isolated from tropical soil. Its properties have been compared to those of other well-characterized cyanophages. In addition, two strains of Anabaena 77S15 lysogenic for N(S)1 were isolated. N(S)1 seems to be integrated into the chromosome of the two lysogens, and a 2 kb plasmid present at a low copy number in the non-lysogenic strain is amplified significantly.     

Investigation of Mannheimia haemolytica bacteriophages relative to host diversity

Aims

This study aimed to characterize the impact of lytic and temperate bacteriophages on the genetic and phenotypic diversity of Mannheimia haemolytica from feedlot cattle.

Methods and Results

Strictly lytic phages were not detected from bovine nasopharyngeal (n = 689) or water trough (n = 30) samples, but Myoviridae‐ or Siphoviridae‐like phages were induced from 54 of 72 M. haemolytica strains by mitomycin C, occasionally from the same strain. Phages with similar restriction fragment length polymorphism profiles (RFLP ≥70% relatedness) shared common host serotypes 1 or 2 (P < 0·000 1). Likewise, phages with similar RFLP tended to occur in genetically related host bacteria (70–79% similarity). Host range assays showed that seven phages from host serotypes 1, 2 and 6 lysed representative strains of serotypes 1, 2 or 8. The genome of vB_MhM_1152AP from serotype 6 was found to be collinear with P2‐like phage φMhaA1‐PHL101.

Conclusions

Prophages are a significant component of the genome of M. haemolytica and contribute significantly to host diversity. Further characterization of the role of prophage in virulence and persistence of M. haemolytica in cattle could provide insight into approaches to control this potential respiratory pathogen.

Significance and Impact of the Study

This study demonstrated that prophages are widespread within the genome of M. haemolytica isolates and emphasized the challenge of isolating lytic phage as a therapeutic against this pathogen.     

Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene

Background

Phages infecting marine picocyanobacteria often carry a psbA gene, which encodes a homolog to the photosynthetic reaction center protein, D1. Host encoded D1 decays during phage infection in the light. Phage encoded D1 may help to maintain photosynthesis during the lytic cycle, which in turn could bolster the production of deoxynucleoside triphosphates (dNTPs) for phage genome replication.

Methodology / Principal Findings

To explore the consequences to a phage of encoding and expressing psbA, we derive a simple model of infection for a cyanophage/host pair — cyanophage P-SSP7 and Prochlorococcus MED4— for which pertinent laboratory data are available. We first use the model to describe phage genome replication and the kinetics of psbA expression by host and phage. We then examine the contribution of phage psbA expression to phage genome replication under constant low irradiance (25 µE m⁻² s⁻¹). We predict that while phage psbA expression could lead to an increase in the number of phage genomes produced during a lytic cycle of between 2.5 and 4.5% (depending on parameter values), this advantage can be nearly negated by the cost of psbA in elongating the phage genome. Under higher irradiance conditions that promote D1 degradation, however, phage psbA confers a greater advantage to phage genome replication.

Conclusions / Significance

These analyses illustrate how psbA may benefit phage in the dynamic ocean surface mixed layer.     

Physicochemical characterization of cyanophage SM-2

Cyanophage SM-2 which infects two unicellular cyanobacteria, Synechococcus elongatus UTEX 563 and Microcystis aeruginosa NRC-1 (Synechococcus sp. NRC-1) UTEX 1937 has a buoyant density of 1.483 g/cm³, a DNA buoyant density of 1.729 g/cm³ and a guanine + cytosine (G+C) content of 69–70%. The protein patterns of cyanophage SM-2 particles showed 11 bands, as determined by polyacrylamide gel electrophoresis, with the bulk of the protein mass concentrated at the 39,000 Mr band. There appear to be no cross-reacting anibodies to whole virus particles of cyanophages SM-1, SM-2 and AS-1. Cyanophage SM-2 requires the presence of cations for viral stability.     

Use of the lambda Red recombinase system to produce recombinant prophages carrying antibiotic resistance genes

Background  

The Red recombinase system of bacteriophage lambda has been used to inactivate chromosomal genes in E. coli K-12 through homologous recombination using linear PCR products. The aim of this study was to induce mutations in the genome of some temperate Shiga toxin encoding bacteriophages. When phage genes are in the prophage state, they behave like chromosomal genes. This enables marker genes, such as antibiotic resistance genes, to be incorporated into the stx gene. Once the phages' lytic cycle is activated, recombinant Shiga toxin converting phages are produced. These phages can transfer the marker genes to the bacteria that they infect and convert. As the Red system's effectiveness decreased when used for our purposes, we had to introduce significant variations to the original method. These modifications included: confirming the stability of the target stx gene increasing the number of cells to be transformed and using a three-step PCR method to produce the amplimer containing the antibiotic resistance gene.     

Use of Real-Time Quantitative PCR for the Analysis of φLC3 Prophage Stability in Lactococci

Bacteriophages are a common and constant threat to proper milk fermentation. It has become evident that lysogeny is widespread in lactic acid bacteria, and in this work the temperate lactococcal bacteriophage LC3 was used as a model to study prophage stability in lactococci. The stability was analyzed in six LC3 lysogenic Lactococcus lactis subsp. cremoris host strains when they were growing at 15 and 30°C. In order to perform these analyses, a real-time PCR assay was developed. The stability of the LC3 prophage was found to vary with the growth phase of its host L. lactis IMN-C1814, in which the induction rate increased during the exponential growth phase and reached a maximum level when the strain was entering the stationary phase. The maximum spontaneous induction frequency of the LC3 prophage varied between 0.32 and 9.1% (28-fold) in the six lysogenic strains. No correlation was observed between growth rates of the host cells and the spontaneous prophage induction frequencies. Furthermore, the level of extrachromosomal phage DNA after induction of the prophage varied between the strains (1.9 to 390%), and the estimated burst sizes varied up to eightfold. These results show that the host cells have a significant impact on the lytic and lysogenic life styles of temperate bacteriophages. The present study shows the power of the real-time PCR technique in the analysis of temperate phage biology and will be useful in work to reveal the impact of temperate phages and lysogenic bacteria in various ecological fields.     

Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer

Background

S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage.

Methodology/Principal Findings

This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces.

Conclusions/Significance

This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene.     

Yet another way that phage λ manipulates its Escherichia coli host: λrexB is involved in the lysogenic–lytic switch

The life cycle of phage λ has been studied extensively. Of particular interest has been the process leading to the decision of the phage to switch from lysogenic to lytic cycle. The principal participant in this process is the λcI repressor, which is cleaved under conditions of DNA damage. Cleaved λcI no longer acts as a repressor, allowing phage λ to switch from its lysogenic to lytic cycle. The well‐known mechanism responsible for λcI cleavage is the SOS response. We have recently reported that the Escherichia coli toxin‐antitoxin mazEF pathway inhibits the SOS response; in fact, the SOS response is permitted only in E. coli strains deficient in the expression of the mazEF pathway. Moreover, in strains lysogenic for prophage λ, the SOS response is enabled by the presence of λrexB. λRexB had previously been found to inhibit the degradation of the antitoxin MazE, thereby preventing the toxic action of MazF. Thus, phage λ rexB gene not only safeguards the prophage state by preventing death of its E. coli host but is also indirectly involved in the lysogenic–lytic switch.     

INTERACTION OF PLECTONEMA BORYANUM (CYANOPHYCEAE) AND THE LPP-CYANOPHAGES IN CONTINUOUS CULTURE1

Continuous culture techniques are used to study long-term population interactions between Plectonema boryanum Gomont, a filamentous bluegreen alga, and the LPP-viruses which infect it. After LPP-I (virulent cyanophage) infection of sensitive algae, 3 oscillations occur in cell density with concomitant oscillations in virus titer before final stabilization of both algal and viral concentrations. After LPP-ID and LPP-2 (temperate viruses) infection, oscillation in cell density occurred with burst of virus particles. Resistant algae always repopulated the chemostat; lysogeny was not established. The interaction between Plectonema that was resistant to virus infection and the 3 LPP-cyanophages resulted in rapid elimination of the viruses from the chemostat in the effluent. When lysogenic P. boryanum was tested, a law population of virus was present in the chemostat throughout the incubation period indicative of spontancous induction. Clones of lysogenic algae were isolated.