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The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order—Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods—including comparative genomics, core genome analysis, and marker gene phylogenetics—to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae—a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order., Systematic Biology, 69 (1), ISSN:1063-5157, ISSN:1076-836X

Mastitis is an inflammation of the mammary gland that occurs when pathogenic microorganisms enter the udder. Even though tremendous advancements in veterinary diagnosis and therapeutics, mastitis is still the most frequent and costly disease of dairy herds overall the world. The purpose of this research was to isolate and identify the lytic phages as a potential method for biological control of bovine mastitis. In this study Klebsiella oxytoca was isolated from contaminated milk samples of Isfahan dairy herds, Isfahan, Iran and characterized as K. oxytoca ABG-IAUF-1 and its 16s-rRNA sequence was deposited in GenBank under the accession numbers of MF175803.1. Then, the four novel specific lytic bacteriophages of K. oxytoca ABG-IAUF-1 from Isfahan public wastewater were isolated and identified. The results of transmission electron microscopy indicated that theses isolated phages were related to Myoviridae and Podoviridae families of bacteriophages. Also the analysis of the growth curve of K. oxytoca ABG-IAUF-1 before and after treatment with lytic phage showed the 97% success rate of the phages in preventing of bacterial growth. This is the first report indicating the use of bacteriophages as the potential agents for eliminating the pathogenic bacteria responsible for bovine mastitis in Iran. The applications of these lytic phages could be an asset for biocontrolling of pathogenic agents in medical and veterinary biotechnology.

International audience; Phages, the viruses of bacteria, have been proposed as antibacterial agents to complement or replace antibiotics due to the growing problem of resistance. In nature and in the clinic, antibiotics are ubiquitous and may affect phages indirectly via impacts on bacterial hosts. Even if the synergistic association of phages and antibiotics has been shown in several studies, the focus is often on bacteria with little known about the impact on phages. Evolutionary studies have demonstrated that time scale is an important factor in understanding the consequences of antimicrobial strategies, but this perspective is generally overlooked in phage-antibiotic combination studies. Here, we explore the effects of antibiotics on phages targeting the opportunistic pathogen Pseudomonas aeruginosa. We go beyond previous studies by testing the interaction between several types of antibiotics and phages, and evaluate the effects on several important phage parameters during 8 days of experimental co-evolution with bacteria. Our study reveals that antibiotics had a negative effect on phage density and efficacy early on, but not in the later stages of the experiment. The results indicate that antibiotics can affect phage adaptation, but that phages can nevertheless contribute to managing antibiotic resistance levels.

Escherichia coli serotype O157: H7 and E. coli O104: H4 are well known foodborne pathogens causing sever enteric illness. Using bacteriophages as biocontrol agents of some foodborne pathogens and multidrug-resistant (MDR) bacteria has a great attention nowadays. This study aims to test the effect of cocktail phages on the growth of some foodborne pathogens and MDR E. coli. Routine conventional PCR was used to confirm the identification of E. coli isolates. Double-layered culture technique was used to isolate phages from sewage water. Morphology of bacteriophage was described using transmission electron microscopy, and spot test was performed to determine host range of the phage cocktail. Phage cocktail of Siphoviridae and Podoviridae family infecting E. coli O157: H7, E. coli O104: H4 and untypeable E. coli (neither O157 nor O104) has been isolated from sewage water. Phage cocktail showed both lytic and lysogenic activity. Lytic activity was observed against E. coli O157: H7, E. coli O104: H4 isolates, Staphylococcus. aureus ATCC6538 and Pseudomonas aeruginosa ATCC 10145, while the lysogenic activity was observed against the untypeable strain. The tested phage cocktail showed a promising inhibitory action on E. coli O157: H7 and O104: H4, S. aureus ATCC6538 and P. aeruginosa ATCC 10145, suggesting the possibility of its use as a biocontrol tool or as natural food preservatives for many food products.

Four lytic bacteriophages designated as φVh1, φVh2, φVh3, and φVh4 were isolated from commercial shrimp hatcheries, possessing broad spectrum of infectivity against luminescent Vibrio harveyi isolates, considering their potential as biocontrol agent of luminescent bacterial disease in shrimp hatcheries, and were characterized by electron microscopy, genomic analysis, restriction enzyme analysis (REA), and pulsed-field gel electrophoresis (PFGE). Three phages φVh1, φVh2, and φVh4 had an icosahedral head of 60-115 nm size with a long, noncontractile tail of 130-329 × 1-17 nm, belonged to the family Siphoviridae. φVh3 had an icosahedral head (72 ± 5 nm) with a short tail (27 × 12 nm) and belonged to Podoviridae. REA with DraI and PFGE of genomic DNA digested with ScaI and XbaI and cluster analysis of their banding patterns indicated that φVh3 was distinct from the other three siphophages. PFGE-based genome mean size of the four bacteriophages φVh1, φVh2, φVh3, and φVh4 was estimated to be about 85, 58, 64, and 107 kb, respectively. These phages had the property of generalized transduction as demonstrated by transduction with plasmid pHSG 396 with frequencies ranging from 4.1 × 10(-7) to 2 × 10(-9) per plaque-forming unit, suggesting a potential ecological role in gene transfer among aquatic vibrios.

Aims: To examine effects of various environmental factors on adsorption and inactivation of Pseudomonas aeruginosa-specific phages: δ (family Podoviridae), J-1, σ-1 and 001A (family Siphoviridae) and their ability to inhibit bacterial growth and biofilm formation. Methods and Results: The phages examined in the study were clonally different, as revealed by RFLP. The temperature in the range 7–44°C had no influence on the adsorption of Podoviridae, but did affect Siphoviridae adsorption, particularly 001A. All phages were significantly stable at pH 5–9, and phages δ and 001A even at pH 3. Most of the examined carbohydrates and exopolysaccharides of the original host efficiently inactivated phage δ, while phages σ-1 and J-1 were inactivated considerably only by the amino acid alanine. Silver nitrate efficiently inactivated all the phages, while Siphoviridae were more resistant to povidone-iodine. Serum of nonimmunized rats had no influence on phage inactivation and adsorption. Only phage δ showed ability to effectively inhibit in vitro bacterial growth and biofilm formation. Conclusions: The examined environmental parameters can significantly influence the adsorption and viability of Ps. aeruginosa-specific phages. The phage δ is a good candidate for biocontrol of Ps. aeruginosa. Significance and Impact of the Study: The study provides important data on Ps. aeruginosa-specific phage adsorption, inactivation and in vitro lytic efficacy.

Aims: To identify enzymes associated with bacteriophages infecting cystic fibrosis (CF) strains of Pseudomonas aeruginosa that are able to degrade extracellular alginic acids elaborated by the host bacterium. Methods and Results: Plaques produced by 21 Ps. aeruginosa-specific phages were screened for the presence of haloes, an indicator of capsule hydrolytic activity. Four phages produced haloed plaques, and one (PT-6) was investigated further. PT-6 was shown by electron microscopy to belong to Podoviridae family C1, to reduce the viscosity of four alginate preparations using a rolling ball viscometer and to release uronic acid-containing fragments from the polymers, as judged by spectrophotometry and thin layer chromatography. The alginase was partially purified by gel filtration chromatography and shown to be a 37 kDa polypeptide. Conclusions: Infection of CF strains of Ps. aeruginosa by phage PT-6 involves hydrolysis of the exopolysaccharide secreted by the host. Significance and Impact of the Study: The alginase produced by PT-6 has the potential to increase the well-being of CF suffers by improving the surface properties of sputum, accelerating phagocytic uptake of bacteria and perturbing bacterial growth in biofilms.

Increases in multidrug-resistant strains of Serratia marcescens are of great concern in pediatrics, especially in neonatal intensive care units. In the search for bacteriophages to control infectious diseases caused by multidrug-resistant S. marcescens, three phages (KSP20, KSP90, and KSP100) were isolated from environmental water and were characterized morphologically and genetically. KSP20 and KSP90 belonged to morphotype A1 of the family Myoviridae, and KSP100 belonged to morphotype C3 of the family Podoviridae. Analysis of the DNA region coding virion proteins, together with their morphological features, indicated that KSP20, KSP90, and KSP100 were related to the P2-like phage (temperate), T4-type phage (virulent), and phiEco32 phage (virulent), respectively. Based on amino acid sequences of the major capsid protein, KSP90 formed a new branch with a Stenotrophomonas maltophilia phage, Smp14, in the T4-type phage phylogeny. Both Smp14 and phiEco32 have been reported as potential therapeutic phages. These results suggest that KSP90 and KSP100 may be candidate therapeutic phages to control S. marcescens infection.

A complete nucleotide sequence of the new Pseudomonas aeruginosa Luz24likevirus phiCHU was obtained. This virus was shown to have a unique host range whereby it grew poorly on the standard laboratory strain PAO1, but infected 26 of 46 clinical isolates screened, and strains harbouring IncP2 plasmid pMG53. It was demonstrated that phiCHU has single-strand interruptions in its genome. Analysis of the phiCHU genome also suggested that recombination event(s) participated in the evolution of the leftmost portion of the genome, presumably encoding early genes.

The first complete nucleotide sequences of two lytic Staphylococcus aureus double stranded DNA phages, 44AHJD (16 784 bp) and P68 (18 227 bp), are reported. Both are small isometric phages, with short, non-contractile tails and a pre-neck appendage. Based on their morphology, their genome size, the similarity of the encoded gene products, the type of infection and on the possession of a type B DNA polymerase, 44AHJD and P68 are allocated to the order Caudovirales , family Podoviridae , genus ‘φ29-like phages’. The genome of 44AHJD differs from that of P68 by a deletion spanning nucleotides 10 091 to 11 531 of the P68 genome. The electrophoretic analysis of the terminal DNA fragments of P68 DNA and P68 DNA protein complex suggested the presence of a terminal protein at either DNA end. In contrast to the lysis cassette of the φ29-like phages, which is located at the end of the late operon, the lysis cassette of 44AHJD and P68 is located within the structural genes.

It has been shown recently that viruses are important agents for the bacterial mortality in marine ecosystems. In this study, 26 bacteriophages were isolated from the Alboran Sea and subsequently characterized in order to determine the diversity of the viral community in this marine environment. All the host bacteria were Gram-negative motile rods, and were unable to grow in media without NaCl. Bacteriophages contained DNA, were not sensitive to chloroform (except phage 16), and showed a close and narrow host range. Morphological studies revealed that most of them were included in two of the three tailed families of the Caudovirales order (viruses belonging to the Podoviridae family were not observed). All bacteriophages had icosahedral heads, the most abundant size class being those ranging from 30 to 60 nm in diameter. The protein profiles of viral clones showed higher variability than that observed by morphological analyses. Phages were grouped in 11 classes on the basis of the protein patterns. In short, phage-host systems analysed in this study are a diverse group and representative of the marine viral community. For this reason, they can be considered as models in studies on the interaction between viral and bacterial communities.

We have explored the nature of the sudden viral amplification observed during the ageing of P22-infected lysogenic colonies of Salmonella typhimurium [Ramírez, E, and Villaverde, A. (1997) Gene 202, 147-149]. By a comparative analysis of the wild-type P22 and a P22 integration mutant, it has been shown that the conditions promoting prophage induction occur in only a small portion of the bacterial population and briefly during the transition between the exponential growth and the stationary phase. The viral burst is RecA-dependent and cannot be reproduced in continuous culture by a mere decrease of the growth rate. This suggests that the limited viral propagation in colonies is probably linked to heterogeneous physiological conditions within colonial populations, distinct from those of the homogeneous liquid cultures.

Natural antisense RNAs have stem-loop (hairpin) secondary structures that are important for their function. The sar antisense RNA of phage P22 is unusual: the 3' half of the molecule forms an extensive stem-loop, but potential structures for the 5' half are not predicted to be thermodynamically stable. We devised a novel method to determine the secondary structure of sar RNA by examining the electrophoretic mobility on non-denaturing gels of numerous sar mutants. The results show that the wild-type RNA forms a 5' stem-loop that enhances electrophoretic mobility. All mutations that disrupt the stem of this hairpin decrease mobility of the RNA. In contrast, mutations that change the sequence of the stem without disrupting it (e.g. change G.U to A.U) do not affect mobility. Nearly all mutations in single-stranded regions of the structure also have no effect on mobility. Confirmation of the proposed 5' stem-loop was obtained by constructing and analyzing compensatory double mutants. Combinations of mutations that restore a base-pair of the stem also restore mobility. The genetic phenotypes of sar mutants confirm that the proposed secondary structure is correct and is essential for optimal activity of the antisense RNA in vivo.

The tailspike protein of bacteriophage P22 assembles with mature capsids during the final reaction in phage morphogenesis. The gene 9 mutation hmH3034 synthesizes a tailspike protein with a change at amino acid 100 from Asp to Asn. This mutant form of trimeric tailspike protein fails to assemble with capsids in vivo. By using in vitro quantitative tailspike-capsid assembly assays, this mutant tailspike trimer can be shown to assemble with capsids at very high tailspike concentrations. From these assays, we estimate that this single missense mutation decreases by 100-500-fold the affinity of the tailspike for capsids. Furthermore, hmH3034 tailspike protein has a structural defect which makes the mature tailspike trimers sensitive to SDS at room temperature and causes the trimers to ``partially unfold.'' Spontaneously arising intragenic suppressors of the capsid assembly defect have been isolated. All of these suppressors are changes at amino acid 13 of the tailspike protein, which substitute His, Leu or Ser for the wild type amino acid Arg. These hmH3034/sup3034 mutants and the separated sup3034 mutants form fully functional tailspike proteins with assembly activities indistinguishable from wild type while retaining the SDS-sensitive structural defect. From the analysis of the hmH3034 mutant and its suppressors, we propose that in the wild-type tailspike protein, the Asp residue at position 100 and the Arg residue at position 13 form an intrachain or interchain salt bridge which stabilizes the amino terminus of the tailspike protein and that the unneutralized positive charge at amino acid 13 in the hmH3034 protein is the cause of the assembly defect of this protein. To test this hypothesis we have generated suppressors of the hmH3034 mutation by site-directed, random mutagenesis of codon 13. From the broad spectrum of amino acids at position 13 which function as suppressors of hmH3034 we have concluded that elimination of Arg at position 13 is sufficient in most cases to restore capsid assembly activity to the hmH3034 protein.

It has been earlier hypothesized that lysogenic infection with Stx-encoding phages influences protein expression in the bacterial host, and therefore, some differentially expressed proteins could affect survival characteristics and pathogenicity. We compared the protein expression profiles of the host MG1655 and lysogens by 2-dimensional electrophoresis. Four different genes identified were all related to Fe/S subunit production, namely, nfuA , fdoH , sdhB , and ftnA . To explore the role of nfuA in the biology of Stx prophage lysogeny, gene knockout experiments and phage lysogenic conversion were performed. The inactivation of nfuA caused the prophage to enter its lytic life cycle, especially under an iron-depleted condition. A similar activity was also detected in the Escherichia coli O157:H7 strain from which the Stx phage Min 27 was originally isolated. NfuA might be the positive regulator of genes controlling lysogenic cycle such as cI , cII and cIII since their transcriptional level was significantly reduced in nfuA deletion mutant as shown by qRT-PCR. We conclude that NfuA is essential for maintenance of Stx phage lysogeny in host's genetic reservoir under iron deficient condition.

The substitution of 2′-fluoro for 2′-hydroxyl moieties in RNA substantially improves the stability of RNA. RNA stability is a major issue in RNA research and applications involving RNA. We report that the RNA polymerase from the marine cyanophage Syn5 has an intrinsic low discrimination against the incorporation of 2′-fluoro dNMPs during transcription elongation. The presence of both magnesium and manganese ions at high concentrations further reduce this discrimination without decreasing the efficiency of incorporation. We have constructed a Syn5 RNA polymerase in which tyrosine 564 is replaced with phenylalanine (Y564F) that further decreases the discrimination against 2 ′-fluoro-dNTPs during RNA synthesis. Sequence elements in DNA templates that affect the yield of RNA and incorporation of 2′-fluoro-dNMPs by Syn5 RNA polymerase have been identified.

Bordetella Bacteriophage (BPP-1) infects both Bordetella bronchiseptica, and B. pertussis, the bacterium that causes whooping cough. BPP-1 is a short-tailed dsDNA virus and a member in the Podoviridae family. It has a T=7 icosahedral head with a diameter of ~700 A and a tail on one of the twelve icosahedral vertices [1]. The capsid head is composed of two proteins: a major capsid protein (MCP) and a cement protein, and neither has recognizable sequence similarity with proteins in other well studied dsDNA bacteriophages like HK97 and PRD1 [2, 3]. We have determined the structure of the icosahedral head of BPP-1 to 3.4A resolution using single particle cryo-electron microscopy (cryoEM) (Fig. 1a) and derived an atomic model of BPP-1. Briefly, cryoEM images were recorded on Kodak SO-163 micrographs at 59K magnification in an FEI Titan Krios microscope at 300kV with a dosage of ~25 e−2/A on the specimen. ~43,000 particles from 340 micrographs were selected for image processing and three dimensional (3D) reconstruction (Fig. 1b, c). Local averaging of the 7 copies of the cement or MCP protein in the asymmetric unit was performed to further improve resolution, model building was performed using Coot, and atomic models were refined using CCP4 (Fig. 1c–e) [4]. Fig. 1 Structure of BPP-1 at 3.4A resolution determined by cryoEM The BPP-1 head reconstruction has an angular shape with 420 MCP subunits making up the capsid shell and 210 dimers of the cement protein joining neighboring MCPs, together forming chainmail (Fig. 1c). Side chains of amino acids are clearly resolved in both proteins and were used for atomic model building. All but the last amino acid of the 140 amino acid residues of the cement protein were visible in the cryoEM density. The atomic model of the cement protein shows a jellyroll fold and a ~40A C-terminal arm (Fig. 1d). The interactions between the two monomers in the cement protein dimer are limited to the F-strand of the jellyroll (Fig. 1d), primarily through a pair of Pro residues, one on each monomer. In contrast, each cement protein monomer interacts with five underlying MCP molecules, mediated through loops of the jellyroll and through a β augmentation of the C-terminal arm (Fig. 1c). This use of the jellyroll fold for an auxiliary stabilizing role is quite remarkable because such fold has only been observed as a building block for viral capsids. Of the 331 residues of the BPP-1 MCP, we traced Thr6 to Val330 in our density map. The N and C termini are both located on the surface, but the first 5 and the last one amino acids are not visible, suggesting their flexibility (Fig. 1e). The BPP-1 MCP has the fold/architecture of the capsid protein of HK97 bacteriophage. We hereby divide it into three building blocks from N to C termini: chainmail-forming (cyan), β sheet-forming (purple) and capsomer-forming (green) (Fig. 1e) [2]. Surprisingly, the topologies of folding these three building blocks into this architecture are different between BPP-1 and HK97 (Fig. 1e, f): The last two of the three building blocks in gp5 of HK97 are swapped as compared to the sequence in BPP-1, in a rare, non-circular permutation, as found in DNA methyltransferases [5]. The difference in the topologies in folding suggests convergent evolution in selecting the characteristic HK97-like fold to build chainmail in the two viruses. It has been found that the internal pressure inside bacteriophages is very high due to the high packing density of the viral genome inside the viral capsid [6], and that different bacteriophages adopt distinctive strategies to stabilize their capsids to withstand the high pressure. HK97 uses covalent isopeptide bonds to link adjacent gp5 proteins to stabilize its capsid [2]. Having the same building blocks but lacking isopeptide bonds to join the chainmail-forming building blocks, BPP-1 uses an extra cement protein with the jellyroll fold to complete the chainmail (Fig. 1c). Our structure highlights the diverse strategies to build a highly stable dsDNA virus and suggests different maturation processes between the two bacteriophages.

Mutations that increase the activity of the promoter for the antirepressor gene of phage P22 were isolated by pseudoreversion of four severe promoter-down mutations. The sequence changes in these pseudorevertants include single base pair substitutions, single base pair deletions, tandem double base pair deletions and multisite mutations. The single base pair substitutions change nonconsensus base pairs to consensus base pairs at positions -14 and -8. The other mutations provide support for the idea that the length of the spacer region between the conserved -35 and -10 hexamers is an important determinant of promoter strength. Deletions of one or two base pairs in the spacer region apparently activate an alternate -10 hexamer by shifting it from a spacing of 19 base pairs to a spacing of 18 or 17 base pairs, respectively.

This paper describes the construction of 18 cloned bacteriophage T7 late promoters with single point mutations. In vitro transcription experiments were used to characterize the properties of these promoters. Since the mutated promoters are cloned into identical backgrounds, differences seen in the transcription assays are directly attributable to the point mutations. All of the mutated promoters are less active than wildtype, but they can be divided into two types. Type A mutations map from -4 to +1 and reduce promoter activity when the template is linearized or when 60mM NaCl is added to the reaction buffer. Type B mutations map from -9 to -7 and reduce promoter activity under all conditions tested. At several sites all three possible point mutations are available. At these sites we observed hierarchies of base pair preference, as determined by promoter activity, that may indicate that T7 RNA polymerase interacts with groups in the major groove.