Genomic organization and molecular characterization of SM1, a temperate bacteriophage of Streptococcus mitis

Approaching In Vivo Models of Pneumococcus-Host Interaction: Insights into Surface Proteins, Capsule Production, and Extracellular Vesicles

Infections caused by the Gram-positive bacterium Streptococcus pneumoniae have become a major health problem worldwide because of their high morbidity and mortality rates, especially in developing countries. This microorganism colonizes the human upper respiratory tract and becomes pathogenic under certain circumstances, which are not well known. In the interaction with the host, bacterial surface structures and proteins play major roles. To gain knowledge into gradual changes and adaptive mechanisms that this pathogen undergoes from when it enters the host, we mimicked several in vivo situations representing interaction with epithelial and macrophage cells, as well as a condition of presence in blood. Then, we analyzed, in four pneumococcal strains, two major surface structures, the capsule and extracellular vesicles produced by the pneumococci, as well as surface proteins by proteomics, using the “shaving” approach, followed by LC-MS/MS. We found important differences in both surface ultrastructures and proteins among the culture conditions and strains used. Thus, this work provides insights into physiological adaptations of the pneumococcus when it interacts with the host, which may be useful for the design of strategies to combat infections caused by this pathogen.

The human oral phageome

Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.

The Bacteriophages of Streptococcus pyogenes

The bacteriophages of Streptococcus pyogenes (group A streptococcus) play a key role in population shaping, genetic transfer, and virulence of this bacterial pathogen. Lytic phages like A25 can alter population distributions through elimination of susceptible serotypes but also serve as key mediators for genetic transfer of virulence genes and antibiotic resistance via generalized transduction. The sequencing of multiple S. pyogenes genomes has uncovered a large and diverse population of endogenous prophages that are vectors for toxins and other virulence factors and occupy multiple attachment sites in the bacterial genomes. Some of these sites for integration appear to have the potential to alter the bacterial phenotype through gene disruption. Remarkably, the phage-like chromosomal islands (SpyCI), which share many characteristics with endogenous prophages, have evolved to mediate a growth-dependent mutator phenotype while acting as global transcriptional regulators. The diverse population of prophages appears to share a large pool of genetic modules that promotes novel combinations that may help disseminate virulence factors to different subpopulations of S. pyogenes. The study of the bacteriophages of this pathogen, both lytic and lysogenic, will continue to be an important endeavor for our understanding of how S. pyogenes continues to be a significant cause of human disease.

The Diverse Impacts of Phage Morons on Bacterial Fitness and Virulence

The viruses that infect bacteria, known as phages, are the most abundant biological entity on earth. They play critical roles in controlling bacterial populations through phage-mediated killing, as well as through formation of bacterial lysogens. In this form, the survival of the phage depends on the survival of the bacterial host in which it resides. Thus, it is advantageous for phages to encode genes that contribute to bacterial fitness and expand the environmental niche. In many cases, these fitness factors also make the bacteria better able to survive in human infections and are thereby considered pathogenesis or virulence factors. The genes that encode these fitness factors, known as "morons," have been shown to increase bacterial fitness through a wide range of mechanisms and play important roles in bacterial diseases. This review outlines the benefits provided by phage morons in various aspects of bacterial life, including phage and antibiotic resistance, motility, adhesion and quorum sensing.

Review manuscript: Mechanisms of platelet activation by the pneumococcus and the role of platelets in community-acquired pneumonia

There is increasing recognition of the involvement of platelets in orchestrating inflammatory responses, driving the activation of neutrophils, monocytes and vascular endothelium, which, if poorly controlled, may lead to microvascular dysfunction. Importantly, hyperreactivity of platelets has been implicated in the pathogenesis of myocardial injury and the associated particularly high prevalence of acute cardiovascular events in patients with severe community-acquired pneumonia (CAP), of which Streptococcus pneumoniae (pneumococcus) is the most commonly encountered aetiologic agent. In this context, it is noteworthy that a number of studies have documented various mechanisms by which the pneumococcus may directly promote platelet aggregation and activation. The major contributors to platelet activation include several different types of pneumococcal adhesin, the pore-forming toxin, pneumolysin, and possibly pathogen-derived hydrogen peroxide, which collectively represent a major focus of the current review. This is followed by an overview of the limited experimental studies together with a larger series of clinical studies mainly focused on all-cause CAP, which have provided evidence in support of associations between alterations in circulating platelet counts, most commonly thrombocytopenia, and a poor clinical outcome. The final section of the review covers, albeit briefly, systemic biomarkers of platelet activation which may have prognostic potential.

A widespread family of polymorphic toxins encoded by temperate phages

Background

Polymorphic toxins (PTs) are multi-domain bacterial exotoxins belonging to distinct families that share common features in terms of domain organization. PTs are found in all major bacterial clades, including many toxic effectors of type V and type VI secretion systems. PTs modulate the dynamics of microbial communities by killing or inhibiting the growth of bacterial competitors lacking protective immunity proteins.

Results

In this work, we identified a novel widespread family of PTs, named MuF toxins, which were exclusively encoded within temperate phages and their prophages. By analyzing the predicted proteomes of 1845 bacteriophages and 2464 bacterial genomes, we found that MuF-containing proteins were frequently part of the DNA packaging module of tailed phages. Interestingly, MuF toxins were abundant in the human gut microbiome.

Conclusions

Our results uncovered the presence of the MuF toxin family in the temperate phages of Firmicutes. The MuF toxin family is likely to play an important role in the ecology of the human microbiota where pathogens and commensal species belonging to the Firmicutes are abundant. We propose that MuF toxins could be delivered by phages into host bacteria and either influence the lysogeny decision or serve as bacterial weapons by inhibiting the growth of competing bacteria.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-017-0415-1) contains supplementary material, which is available to authorized users.

YMC-2011, a Temperate Phage of Streptococcus salivarius 57.I

Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally, with an estimated copy number of 3 to 4. Phage particles were isolated from the supernatant of mitomycin C-treated S. salivarius 57.I cultures, and transmission electron microscopic examination indicated that YMC-2011 belongs to the Siphoviridae family. Phylogenetic analysis suggests that phage YMC-2011 and the cos-type phages of Streptococcus thermophilus originated from a common ancestor. An extended -10 element (p _L ) and a σ⁷⁰-like promoter (p _R ) were mapped 5' to Ssal_phage00013 (encoding a CI-like repressor) and Ssal_phage00014 (encoding a hypothetical protein), respectively, using 5' rapid amplification of cDNA ends, indicating that YMC-2011 transcribes at least two mRNAs in opposite orientations. Studies using promoter-chloramphenicol acetyltransferase reporter gene fusions revealed that p _R , but not p _L , was sensitive to mitomycin C induction, suggesting that the switch from lysogenic growth to lytic growth was controlled mainly by the activity of these two promoters. In conclusion, a lysogenic state is maintained in S. salivarius 57.I, presumably by the repression of genes encoding proteins for lytic growth.IMPORTANCE The movement of mobile genetic elements such as bacteriophages and the establishment of lysogens may have profound effects on the balance of microbial ecology where lysogenic bacteria reside. The discovery of phage YMC-2011 from Streptococcus salivarius 57.I suggests that YMC-2011 and Streptococcus thermophilus-infecting phages share an ancestor. Although S. salivarius and S. thermophilus are close phylogenetically, S. salivarius is a natural inhabitant of the human mouth, whereas S. thermophilus is commonly found in the mammary mucosa of bovine species. Thus, the identification of YMC-2011 suggests that horizontal gene transfer via phage infection could take place between species from different ecological niches.

The use of bacteriophages to biocontrol oral biofilms

Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and expenditure. As bacterial biofilms are highly resistant and resilient to conventional antibacterial therapy, it has been difficult to combat these infections. An innovative alternative to the biocontrol of oral biofilms could be to use bacteriophages or phages, the viruses of bacteria, which are specific, non-toxic, self-proliferating, and can penetrate into biofilms. Phages for Actinomyces naeslundii, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Fusobacterium nucleatum, Lactobacillus spp., Neisseria spp., Streptococcus spp., and Veillonella spp. have been isolated and characterised. Recombinant phage enzymes (lysins) have been shown to lyse A. naeslundii and Streptococcus spp. However, only a tiny fraction of available phages and their lysins have been explored so far. The unique properties of phages and their lysins make them promising but challenging antimicrobials. The genetics and biology of phages have to be further explored in order to determine the most effective way of applying them. Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy.

Diverse virulent pneumophages infect Streptococcus mitis

Streptococcus mitis has emerged as one of the leading causes of bacterial endocarditis and is related to Streptococcus pneumoniae. Antibiotic resistance has also increased among strains of S. mitis and S. pneumoniae. Phages are being reinvestigated as alternatives to antibiotics for managing infections. In this study, the two virulent phages Cp-1 (Podoviridae) and Dp-1 (Siphoviridae), previously isolated from S. pneumoniae, were found to also infect S. mitis. Microbiological assays showed that both pneumophages could not only replicate in S. mitis but also produced more visible plaques on this host. However, the burst size and phage adsorption data were lower in S. mitis as compared to S. pneumoniae. A comparison of the genomes of each phage grown on both hosts produced identical nucleotide sequences, confirming that the same phages infect both bacterial species. We also discovered that the genomic sequence of podophage Cp-1 of the Félix d'Hérelle collection is different than the previously reported sequence and thus renamed SOCP.

Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions

Bacteriophages and genetic elements, such as prophage-like elements, pathogenicity islands, and phage morons, make up a considerable amount of bacterial genomes. Their transfer and subsequent activity within the host's genetic circuitry have had a significant impact on bacterial evolution. In this review, we consider what underlying mechanisms might cause the spontaneous activity of lysogenic phages in single bacterial cells and how the spontaneous induction of prophages can lead to competitive advantages for and influence the lifestyle of bacterial populations or the virulence of pathogenic strains.

Genome-based approaches to develop epitope-driven subunit vaccines against pathogens of infective endocarditis

Infective endocarditis (IE) has emerged as a public health problem due to changes in the etiologic spectrum and due to involvement of resistant bacterial strains with increased virulence. Developing potent vaccine is an important strategy to tackle IE. Complete genome sequences of eight selected pathogens of IE paved the way to design common T-cell driven subunit vaccines. Comparative genomics and subtractive genomic analysis were applied to identify adinosine tri phosphate (ATP)-binding cassette (ABC) transporter ATP-binding protein from Streptococcus mitis (reference organism) as common vaccine target. Reverse vaccinology technique was implemented using computational tools such as ProPred, SYFPEITHI, and Immune epitope database. Twenty-one T-cell epitopes were predicted from ABC transporter ATP-binding protein. Multiple sequence alignment of ABC transporter ATP-binding protein from eight selected IE pathogens was performed to identify six conserved T-cell epitopes. The six selected T-cell epitopes were further evaluated at structure level for HLA-DRB binding through homology modeling and molecular docking analysis using Maestro v9.2. The proposed six T-cell epitopes showed better binding affinity with the selected HLA-DRB alleles. Subsequently, the docking complexes of T-cell epitope and HLA-DRBs were ranked based on XP Gscore. The T-cell epitope (208-LNYITPDVV-216)-HLA-DRB1(∗)0101 (1T5 W) complex having the best XP Gscore (-13.25 kcal/mol) was assessed for conformational stability and interaction stability through molecular dynamic simulation for 10 ns using Desmond v3.2. The simulation results revealed that the HLA-DRB-epitope complex was stable throughout the simulation time. Thus, the epitope would be ideal candidate for T-cell driven subunit vaccine design against infective endocarditis.

Bacteriophage-encoded bacterial virulence factors and phage-pathogenicity island interactions

The role of bacteriophages as natural vectors for some of the most potent bacterial toxins is well recognized and includes classical type I membrane-acting superantigens, type II pore-forming lysins, and type III exotoxins, such as diphtheria and botulinum toxins. Among Gram-negative pathogens, a novel class of bacterial virulence factors called effector proteins (EPs) are phage encoded among pathovars of Escherichia coli, Shigella spp., and Salmonella enterica. This chapter gives an overview of the different types of virulence factors encoded within phage genomes based on their role in bacterial pathogenesis. It also discusses phage-pathogenicity island interactions uncovered from studies of phage-encoded EPs. A detailed examination of the filamentous phage CTXφ that encodes cholera toxin is given as the sole example to date of a single-stranded DNA phage that encodes a bacterial toxin.

Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate

Background

Streptococcus pneumoniae is an important human pathogen representing a major cause of morbidity and mortality worldwide. We sequenced the genome of a serotype 11A, ST62 S. pneumoniae invasive isolate (AP200), that was erythromycin-resistant due to the presence of the erm(TR) determinant, and carried out analysis of the genome organization and comparison with other pneumococcal genomes.

Results

The genome sequence of S. pneumoniae AP200 is 2,130,580 base pair in length. The genome carries 2216 coding sequences (CDS), 56 tRNA, and 12 rRNA genes. Of the CDSs, 72.9% have a predicted biological known function. AP200 contains the pilus islet 2 and, although its phenotype corresponds to serotype 11A, it contains an 11D capsular locus. Chromosomal rearrangements resulting from a large inversion across the replication axis, and horizontal gene transfer events were observed. The chromosomal inversion is likely implicated in the rebalance of the chromosomal architecture affected by the insertions of two large exogenous elements, the erm(TR)-carrying Tn1806 and a functional prophage designated ϕSpn_200. Tn1806 is 52,457 bp in size and comprises 49 ORFs. Comparative analysis of Tn1806 revealed the presence of a similar genetic element or part of it in related species such as Streptococcus pyogenes and also in the anaerobic species Finegoldia magna, Anaerococcus prevotii and Clostridium difficile. The genome of ϕSpn_200 is 35,989 bp in size and is organized in 47 ORFs grouped into five functional modules. Prophages similar to ϕSpn_200 were found in pneumococci and in other streptococcal species, showing a high degree of exchange of functional modules. ϕSpn_200 viral particles have morphologic characteristics typical of the Siphoviridae family and are capable of infecting a pneumococcal recipient strain.

Conclusions

The sequence of S. pneumoniae AP200 chromosome revealed a dynamic genome, characterized by chromosomal rearrangements and horizontal gene transfers. The overall diversity of AP200 is driven mainly by the presence of the exogenous elements Tn1806 and ϕSpn_200 that show large gene exchanges with other genetic elements of different bacterial species. These genetic elements likely provide AP200 with additional genes, such as those conferring antibiotic-resistance, promoting its adaptation to the environment.

The annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes

φEf11 is a temperate Siphoviridae bacteriophage isolated by induction from a lysogenic Enterococcus faecalis strain. The φEf11 DNA was completely sequenced and found to be 42,822 bp in length, with a G+C mol% of 34.4%. Genome analysis revealed 65 ORFs, accounting for 92.8% of the DNA content. All except for seven of the ORFs displayed sequence similarities to previously characterized proteins. The genes were arranged in functional modules, organized similar to that of several other phages of low GC Gram-positive bacteria; however, the number and arrangement of lysis-related genes were atypical of these bacteriophages. A 159 bp noncoding region between predicted cI and cro genes is highly similar to the functionally characterized early promoter region of lactococcal temperate phage TP901-1, and possessed a predicted stem-loop structure in between predicted P(L) and P(R) promoters, suggesting a novel mechanism of repression of these two bacteriophages from the λ paradigm. Comparison with all available phage and predicted prophage genomes revealed that the φEf11 genome displays unique features, suggesting that φEf11 may be a novel member of a larger family of temperate prophages that also includes lactococcal phages. Trees based on the blast score ratio grouped this family by tail fiber similarity, suggesting that these trees are useful for identifying phages with similar tail fibers.

Streptococcus mitis: walking the line between commensalism and pathogenesis

Streptococcus mitis is a viridans streptococcus and a normal commensal of the human oropharynx. However, S. mitis can escape from this niche and cause a variety of infectious complications including infective endocarditis, bacteraemia and septicaemia. It uses a variety of strategies to effectively colonize the human oropharynx. These include expression of adhesins, immunoglobulin A proteases and toxins, and modulation of the host immune system. These various colonization factors allow S. mitis to compete for space and nutrients in the face of its more pathogenic oropharyngeal microbial neighbours. However, it is likely that in vulnerable immune-compromised patients S. mitis will use the same colonization and immune modulation factors as virulence factors promoting its opportunistic pathogenesis. The recent publication of a complete genome sequence for S. mitis strain B6 will allow researchers to thoroughly investigate which genes are involved in S. mitis host colonization and pathogenesis. Moreover, it will help to give insight into where S. mitis fits in the complicated oral microbiome. This review will discuss the current knowledge of S. mitis factors involved in host colonization, their potential role in virulence and what needs to be done to fully understand how a an oral commensal successfully transitions to a virulent pathogen.

Genome sequence of the temperate bacteriophage PH10 from Streptococcus oralis

Exponential growing cultures of Streptococcus oralis strain OMZ 1038, isolated from human supragingival dental plaque, were found to release a bacteriophage (designated PH10) upon treatment with mitomycin C. The complete genome sequence of phage PH10 was determined. The genome was 31276 bp in size and contained 54 open reading frames. The module encoding structural proteins was highly similar to that of Streptococcus pneumoniae prophage PhiSpn_3. The most abundant phage structural protein was encoded by ORF35 and was likely processed by proteolytic cleavage. The putative endolysin from PH10, which contained a muramidase domain and a choline-binding domain, was purified and shown to have lytic activity with S. oralis, S. pneumoniae and Streptococcus mitis, but not with other streptococcal species.

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

The human oropharynx is a reservoir for many potential pathogens, including streptococcal species that cause endocarditis. Although oropharyngeal microbes have been well described, viral communities are essentially uncharacterized. We conducted a metagenomic study to determine the composition of oropharyngeal DNA viral communities (both phage and eukaryotic viruses) in healthy individuals and to evaluate oropharyngeal swabs as a rapid method for viral detection. Viral DNA was extracted from 19 pooled oropharyngeal swabs and sequenced. Viral communities consisted almost exclusively of phage, and complete genomes of several phage were recovered, including Escherichia coli phage T3, Propionibacterium acnes phage PA6, and Streptococcus mitis phage SM1. Phage relative abundances changed dramatically depending on whether samples were chloroform treated or filtered to remove microbial contamination. pblA and pblB genes of phage SM1 were detected in the metagenomes. pblA and pblB mediate the attachment of S. mitis to platelets and play a significant role in S. mitis virulence in the endocardium, but have never previously been detected in the oral cavity. These genes were also identified in salivary metagenomes from three individuals at three time points and in individual saliva samples by PCR. Additionally, we demonstrate that phage SM1 can be induced by commonly ingested substances. Our results indicate that the oral cavity is a reservoir for pblA and pblB genes and for phage SM1 itself. Further studies will determine the association between pblA and pblB genes in the oral cavity and the risk of endocarditis.

Streptococcus mitis phage-encoded adhesins mediate attachment to {alpha}2-8-linked sialic acid residues on platelet membrane gangliosides

The direct binding of bacteria to human platelets contributes to the pathogenesis of infective endocarditis. Platelet binding by Streptococcus mitis strain SF100 is mediated in part by two bacteriophage-encoded proteins, PblA and PblB. However, the platelet membrane receptor for these adhesins has been unknown. In this study, we demonstrate that these proteins mediate attachment of bacterial cells to sialylated gangliosides on the platelet cell surface. Desialylation of human platelet monolayers reduced adherence of SF100, whereas treatment of the platelets with N- or O-glycanases did not affect platelet binding. Treatment of platelets with sialidases having different linkage specificities showed that removal of alpha2-8-linked sialic acids resulted in a marked reduction in bacterial binding. Preincubation of SF100 with ganglioside GD3, a glycolipid containing alpha2-8-linked sialic acids that is present on platelet membranes, blocked subsequent binding of this strain to these cells. In contrast, GD3 had no effect on the residual binding of platelets by strain PS344, an isogenic DeltapblA DeltapblB mutant. Preincubating platelets with specific monoclonal antibodies to ganglioside GD3 also inhibited binding of SF100 to platelets, but again, they had no effect on binding by PS344. When the direct binding of S. mitis strains SF100 and PS344 to immobilized gangliosides was tested, binding of PS344 to GD3 was reduced by 70% compared to the parent strain. These results indicated that platelet binding by SF100 is mediated by the interaction of PblA and PblB with alpha2-8-linked sialic acids on ganglioside GD3.

Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages

Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage phiSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them.

Development of a prophage typing system and analysis of prophage carriage in Streptococcus pneumoniae

The frequency of prophage carriage was tested in a collection of 108 clinical isolates of Streptococcus pneumoniae. A PCR-based assay was developed to allow classification of the prophage into the three groups recently identified according to genome comparisons (P. Romero, N. Croucher, N. L. Hiller, F. Z. Hu, G. D. Ehrlich, S. D. Bentley, E. García, and T. J. Mitchell, submitted for publication). Use of the assay showed that more than half of the isolates studied were lysogenic with prophage belonging to group 1 being the most abundant (56%), followed by those belonging to group 2 (26%) and those belonging to group 3 (11%). Four polylysogenic strains harboring a group 1 and a group 2 prophage were identified. Interestingly, lysogenic strains were found in 8 out of the 12 internationally distributed, relevant clones of S. pneumoniae contained in our strain collection. The high percentage of clinical pneumococcal isolates harboring prophage strongly suggests an important contribution to the diversification of the genome architecture in this species as well as a role for bacteriophage in the virulence/and or fitness of S. pneumoniae, although further studies using a significant number of isolates belonging to the most relevant pneumococcal clones are needed.

Mechanism of cell surface expression of the Streptococcus mitis platelet binding proteins PblA and PblB

PblA and PblB are prophage-encoded proteins of Streptococcus mitis strain SF100 that mediate binding to human platelets. The mechanism for surface expression of these proteins has been unknown, as they do not contain signal sequences or cell wall sorting motifs. We therefore assessed whether expression of these proteins was linked the lytic cycle of the prophage. Deletion of either the holin or lysin gene resulted in retention of PblA and PblB in the cytoplasm, and loss of these proteins from the cell wall. Flow cytometric analysis revealed that induction of phage replication in SF100 produced a subpopulation of cells with increased permeability. This effect was abrogated by disruption of the holin and lysin genes. Treatment of these mutants with exogenous PblA and PblB restored surface expression, apparently via binding of the proteins to cell wall choline. Loss of PblA and PblB expression was associated with decreased platelet binding in vitro, and reduced virulence in an animal model of endocarditis. Thus, expression of PblA and PblB occurs via a novel mechanism, whereby phage induction increases bacterial permeability and release of the proteins, followed by their binding to surface of viable cells. This mechanism may be important for endovascular infection.

Genome sequence of Streptococcus mutans bacteriophage M102

Bacteriophage M102 is a lytic phage specific for serotype c strains of Streptococcus mutans, a causative agent of dental caries. In this study, the complete genome sequence of M102 was determined. The genome is 31,147 bp in size and contains 41 ORFs. Most of the ORFs encoding putative phage structural proteins show similarity to those from bacteriophages from Streptococcus thermophilus. Bioinformatic analysis indicated that the M102 genome contains an unusual lysis cassette, which encodes a holin and two lytic enzymes.

Curated list of prokaryote viruses with fully sequenced genomes

Genome sequencing is of enormous importance for classification of prokaryote viruses and for understanding the evolution of these viruses. This survey covers 284 sequenced viruses for which a full description has been published and for which the morphology is known. This corresponds to 219 (4%) of tailed and 75 (36%) of tailless viruses of prokaryotes. The number of sequenced tailless viruses almost doubles if viruses of unknown morphology are counted. The sequences are from representatives of 15 virus families and three groups without family status, including eight taxa of archaeal viruses. Tailed phages, especially those with large genomes and hosts other than enterobacteria or lactococci, mycobacteria and pseudomonads, are vastly under investigated.

Isolation and sequencing of a temperate transducing phage for Pasteurella multocida

A temperate bacteriophage (F108) has been isolated through mitomycin C induction of a Pasteurella multocida serogroup A strain. F108 has a typical morphology of the family Myoviridae, presenting a hexagonal head and a long contractile tail. F108 is able to infect all P. multocida serogroup A strains tested but not those belonging to other serotypes. Bacteriophage F108, the first P. multocida phage sequenced so far, presents a 30,505-bp double-stranded DNA genome with cohesive ends (CTTCCTCCCC cos site). The F108 genome shows the highest homology with those of Haemophilus influenzae HP1 and HP2 phages. Furthermore, an F108 prophage attachment site in the P. multocida chromosome has been established to be inside a gene encoding tRNA(Leu). By using several chromosomal markers that are spread along the P. multocida chromosome, it has been demonstrated that F108 is able to perform generalized transduction. This fact, together with the absence of pathogenic genes in the F108 genome, makes this bacteriophage a valuable tool for P. multocida genetic manipulation.

Isolation and expression of the lysis genes of Actinomyces naeslundii phage Av-1

Like most gram-positive oral bacteria, Actinomyces naeslundii is resistant to salivary lysozyme and to most other lytic enzymes. We are interested in studying the lysins of phages of this important oral bacterium as potential diagnostic and therapeutic agents. To identify the Actinomyces phage genes encoding these species-specific enzymes in Escherichia coli, we constructed a new cloning vector, pAD330, that can be used to enrich for and isolate phage holin genes, which are located adjacent to the lysin genes in most phage genomes. Cloned holin insert sequences were used to design sequencing primers to identify nearby lysin genes by using whole phage DNA as the template. From partial digestions of A. naeslundii phage Av-1 genomic DNA we were able to clone, in independent experiments, inserts that complemented the defective lambda holin in pAD330, as evidenced by extensive lysis after thermal induction. The DNA sequence of the inserts in these plasmids revealed that both contained the complete lysis region of Av-1, which is comprised of two holin-like genes, designated holA and holB, and an endolysin gene, designated lysA. We were able to subclone and express these genes and determine some of the functional properties of their gene products.

Genomic organization and molecular analysis of virulent bacteriophage 2972 infecting an exopolysaccharide-producing Streptococcus thermophilus strain

The Streptococcus thermophilus virulent pac-type phage 2972 was isolated from a yogurt made in France in 1999. It is a representative of several phages that have emerged with the industrial use of the exopolysaccharide-producing S. thermophilus strain RD534. The genome of phage 2972 has 34,704 bp with an overall G+C content of 40.15%, making it the shortest S. thermophilus phage genome analyzed so far. Forty-four open reading frames (ORFs) encoding putative proteins of 40 or more amino acids were identified, and bioinformatic analyses led to the assignment of putative functions to 23 ORFs. Comparative genomic analysis of phage 2972 with the six other sequenced S. thermophilus phage genomes confirmed that the replication module is conserved and that cos- and pac-type phages have distinct structural and packaging genes. Two group I introns were identified in the genome of 2972. They interrupted the genes coding for the putative endolysin and the terminase large subunit. Phage mRNA splicing was demonstrated for both introns, and the secondary structures were predicted. Eight structural proteins were also identified by N-terminal sequencing and/or matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Detailed analysis of the putative minor tail proteins ORF19 and ORF21 as well as the putative receptor-binding protein ORF20 showed the following interesting features: (i) ORF19 is a hybrid protein, because it displays significant identity with both pac- and cos-type phages; (ii) ORF20 is unique; and (iii) a protein similar to ORF21 of 2972 was also found in the structure of the cos-type phage DT1, indicating that this structural protein is present in both S. thermophilus phage groups. The implications of these findings for phage classification are discussed.

Recent trends on the molecular biology of pneumococcal capsules, lytic enzymes, and bacteriophage

Streptococcus pneumoniae has re-emerged as a major cause of morbidity and mortality throughout the world and its continuous increase in antimicrobial resistance is rapidly becoming a leading cause of concern for public health. This review is focussed on the analysis of recent insights on the study of capsular polysaccharide biosynthesis, and cell wall (murein) hydrolases, two fundamental pneumococcal virulence factors. Besides, we have also re-evaluated the molecular biology of the pneumococcal phage, their possible role in pathogenicity and in the shaping of natural populations of S. pneumoniae. Precise knowledge of the topics reviewed here should facilitate the rationale to move towards the design of alternative ways to combat pneumococcal disease.

Characterization of LytA-like N-acetylmuramoyl-L-alanine amidases from two new Streptococcus mitis bacteriophages provides insights into the properties of the major pneumococcal autolysin

Two new temperate bacteriophages exhibiting a Myoviridae (phiB6) and a Siphoviridae (phiHER) morphology have been isolated from Streptococcus mitis strains B6 and HER 1055, respectively, and partially characterized. The lytic phage genes were overexpressed in Escherichia coli, and their encoded proteins were purified. The lytAHER and lytAB6 genes are very similar (87% identity) and appeared to belong to the group of the so-called typical LytA amidases (atypical LytA displays a characteristic two-amino-acid deletion signature). although they exhibited several differential biochemical properties with respect to the pneumococcal LytA, e.g., they were inhibited in vitro by sodium deoxycholate and showed a more acidic pH for optimal activity. However, and in sharp contrast with the pneumococcal LytA, a short dialysis of LytAHER or LytAB6 resulted in reversible deconversion to the low-activity state (E-form) of the fully active phage amidases (C-form). Comparison of the amino acid sequences of LytAHER and LytAB6 with that of the pneumococcal amidase suggested that Val317 might be responsible for at least some of the peculiar properties of S. mitis phage enzymes. Site-directed mutagenesis that changed Val317 in the pneumococcal LytA amidase to a Thr residue (characteristic of LytAB6 and LytAHER) produced a fully active pneumococcal enzyme that differs from the parental one only in that the mutant amidase can reversibly recover the low-activity E-form upon dialysis. This is the first report showing that a single amino acid residue is involved in the conversion process of the major S. pneumoniae autolysin. Our results also showed that some lysogenic S. mitis strains possess a lytA-like gene, something that was previously thought to be exclusive to Streptococcus pneumoniae. Moreover, the newly discovered phage lysins constitute a missing link between the typical and atypical pneumococcal amidases known previously.