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Genome Sequencing Reveals a Phage in Helicobacter pylori
Lehours, Philippe
Vale, Filipa F.
Bjursell, Magnus K.
Melefors, Ojar
Advani, Reza
Glavas, Steve
Guegueniat, Julia
Gontier, Etienne
Lacomme, Sabrina
Alves Matos, António
Menard, Armelle
Mégraud, Francis
Engstrand, Lars
Andersson, Anders F.
Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. Genomic analysis of several strains has revealed an extensive H. pylori pan-genome, likely to grow as more genomes are sampled. Here we describe the draft genome sequence (63 contigs; 26× mean coverage) of H. pylori strain B45, isolated from a patient with gastric mucosa-associated lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage integrated in the bacterial genome. The prophage shares most of its genes (22/27) with prophage region II of Helicobacter acinonychis strain Sheeba. After UV treatment of liquid cultures, circular DNA carrying the prophage integrase gene could be detected, and intracellular tailed phage-like particles were observed in H. pylori cells by transmission electron microscopy, indicating that phage production can be induced from the prophage. PCR amplification and sequencing of the integrase gene from 341 H. pylori strains from different geographic regions revealed a high prevalence of the prophage (21.4%). Phylogenetic reconstruction showed four distinct clusters in the integrase gene, three of which tended to be specific for geographic regions. Our study implies that phages may play important roles in the ecology and evolution of H. pylori.
Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population, and while most of the infected individuals do not develop disease, H. pylori infection doubles the risk of developing gastric cancer. An abundance and diversity of viruses (phages) infect microbial populations in most environments and are important mediators of microbial diversity. Our finding of a 24.6-kb prophage integrated inside an H. pylori genome and the observation of circular integrase gene-containing DNA and phage-like particles inside cells upon UV treatment demonstrate that we have discovered a viable H. pylori phage. The additional finding of integrase genes in a large proportion of screened isolates of diverse geographic origins indicates that the prevalence of prophages may have been underestimated in H. pylori. Since phages are important drivers of microbial evolution, the discovery should be important for understanding and predicting genetic diversity in H. pylori.
Related Articles
Origins of the Xylella fastidiosa Prophage-Like Regions and Their Impact in Genome Differentiation
de Mello Varani, Alessandro
Souza, Rangel Celso
Nakaya, Helder I.
de Lima, Wanessa Cristina
Paula de Almeida, Luiz Gonzaga
Kitajima, Elliot Watanabe
Chen, Jianchi
Civerolo, Edwin
Vasconcelos, Ana Tereza Ribeiro
Van Sluys, Marie-Anne
PLoS ONE
Xylella fastidiosa is a Gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced X. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. To better evaluate the recent evolution of the X. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and Temecula1), and in two candidate molecules (Ann1 and Dixon) were assessed. Based on comparative best bidirectional hit analyses, the majority (51%) of the predicted genes in the X. fastidiosa prophage-like regions are related to structural phage genes belonging to the Siphoviridae family. Electron micrograph reveals the existence of putative viral particles with similar morphology to lambda phages in the bacterial cell in planta. Moreover, analysis of microarray data indicates that 9a5c strain cultivated under stress conditions presents enhanced expression of phage anti-repressor genes, suggesting switches from lysogenic to lytic cycle of phages under stress-induced situations. Furthermore, virulence-associated proteins and toxins are found within these prophage-like elements, thus suggesting an important role in host adaptation. Finally, clustering analyses of phage integrase genes based on multiple alignment patterns reveal they group in five lineages, all possessing a tyrosine recombinase catalytic domain, and phylogenetically close to other integrases found in phages that are genetic mosaics and able to perform generalized and specialized transduction. Integration sites and tRNA association is also evidenced. In summary, we present comparative and experimental evidence supporting the association and contribution of phage activity on the differentiation of Xylella genomes.
Related Articles
Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity
Fouts, Derrick E
Klumpp, Jochen
Bishop-Lilly, Kimberly A
Rajavel, Mathumathi
Willner, Kristin M
Butani, Amy
Henry, Matthew
Biswas, Biswajit
Li, Manrong
Albert, M John
Loessner, Martin J
Calendar, Richard
Sozhamannan, Shanmuga
Virology Journal
Vibrio cholerae O139 Bengal is the only serogroup other than O1 implicated in cholera epidemics. We describe the isolation and characterization of an O139 serogroup-specific phage, vB_VchP_VchO139-I (ϕVchO139-I) that has similar host range and virion morphology as phage vB_VchP_JA1 (ϕJA1) described previously. We aimed at a complete molecular characterization of both phages and elucidation of their genetic and structural differences and assessment of their genetic relatedness to the N4-like phage group.
Host-range analysis and plaque morphology screening were done for both ϕJA1 and ϕVchO139-I. Both phage genomes were sequenced by a 454 and Sanger hybrid approach. Genomes were annotated and protein homologies were determined by Blast and HHPred. Restriction profiles, PFGE patterns and data on the physical genome structure were acquired and phylogenetic analyses were performed.
The host specificity of ϕJA1 has been attributed to the unique capsular O-antigen produced by O139 strains. Plaque morphologies of the two phages were different; ϕVchO139-I produced a larger halo around the plaques than ϕJA1. Restriction profiles of ϕJA1 and ϕVchO139-I genomes were also different. The genomes of ϕJA1 and ϕVchO139-I consisted of linear double-stranded DNA of 71,252 and 70,938 base pairs. The presence of direct terminal repeats of around 1974 base pairs was demonstrated. Whole genome comparison revealed single nucleotide polymorphisms, small insertions/deletions and differences in gene content. Both genomes had 79 predicted protein encoding sequences, of which only 59 were identical between the two closely related phages. They also encoded one tRNA-Arg gene, an intein within the large terminase gene, and four homing endonuclease genes. Whole genome phylogenetic analyses of ϕJA1 and ϕVchO139-I against other sequenced N4-like phages delineate three novel subgroups or clades within this phage family.
The closely related phages feature significant genetic differences, in spite of being morphologically identical. The phage morphology, genetic organization, genomic content and large terminase protein based phylogeny support the placement of these two phages in the Podoviridae family, more specifically within the N4-like phage group. The physical genome structure of ϕJA1 could be demonstrated experimentally. Our data pave the way for potential use of ϕJA1 and ϕVchO139-I in Vibrio cholerae typing and control.
Vibrio cholerae O139; N4-like virus; Genome comparison; Terminal repeats; Intein; Phylogenetic relationship
Related Articles
Evolution of Immunity and Host Chromosome Integration Site of P2-Like Coliphages
Karlsson, Joakim L.
Cardoso-Palacios, Carlos
Nilsson, Anders S.
Haggård-Ljungquist, Elisabeth
Journal of Bacteriology
The amount and distribution of variation in the genomic region containing the genes in the lytic-lysogenic genetic switch and the sequence that determines the integration site into the host chromosome were analyzed for 38 P2-like phages from Escherichia coli. The genetic switch consists of two convergent mutually exclusive promoters, Pe and Pc, and two repressors, C and Cox. The immunity repressor C blocks the early Pe promoter, leading to the establishment of lysogeny. The Cox repressor blocks expression of Pc, allowing lytic growth. Phylogenetic analyses showed that the C and Cox proteins were distributed into seven distinct classes. The phylogenetic relationship differed between the two proteins, and we showed that homologous recombination plays a major role in creating alterations in the genetic switch, leading to new immunity classes. Analyses of the host integration site for these phages resulted in the discovery of a previously unknown site, and there were at least four regular integration sites. Interestingly, we found no case where phages of the same immunity class had different host attachment sites. The evolution of immunity and integration sites is complex, since it involves interactions both between the phages themselves and between phages and hosts, and often, both regulatory proteins and target DNA must change.
Related Articles
The Dilemma of Phage Taxonomy Illustrated by Comparative Genomics of Sfi21-Like Siphoviridae in Lactic Acid Bacteria
Proux, Caroline
van Sinderen, Douwe
Suarez, Juan
Garcia, Pilar
Ladero, Victor
Fitzgerald, Gerald F.
Desiere, Frank
Brüssow, Harald
Journal of Bacteriology
The complete genome sequences of two dairy phages, Streptococcus thermophilus phage 7201 and Lactobacillus casei phage A2, are reported. Comparative genomics reveals that both phages are members of the recently proposed Sfi21-like genus of Siphoviridae, a widely distributed phage type in low-GC-content gram-positive bacteria. Graded relatedness, the hallmark of evolving biological systems, was observed when different Sfi21-like phages were compared. Across the structural module, the graded relatedness was represented by a high level of DNA sequence similarity or protein sequence similarity, or a shared gene map in the absence of sequence relatedness. This varying range of relatedness was found within Sfi21-like phages from a single species as demonstrated by the different prophages harbored by Lactococcus lactis strain IL1403. A systematic dot plot analysis with 11 complete L. lactis phage genome sequences revealed a clear separation of all temperate phages from two classes of virulent phages. The temperate lactococcal phages share DNA sequence homology in a patchwise fashion over the nonstructural gene cluster. With respect to structural genes, four DNA homology groups could be defined within temperate L. lactis phages. Closely related structural modules for all four DNA homology groups were detected in phages from Streptococcus or Listeria, suggesting that they represent distinct evolutionary lineages that have not uniquely evolved in L. lactis. It seems reasonable to base phage taxonomy on data from comparative genomics. However, the peculiar modular nature of phage evolution creates ambiguities in the definition of phage taxa by comparative genomics. For example, depending on the module on which the classification is based, temperate lactococcal phages can be classified as a single phage species, as four distinct phage species, or as two if not three different phage genera. We propose to base phage taxonomy on comparative genomics of a single structural gene module (head or tail genes). This partially phylogeny-based taxonomical system still mirrors some aspects of the current International Committee on Taxonomy in Virology classification system. In this system the currently sequenced lactococcal phages would be grouped into five genera: c2-, sk1, Sfi11-, r1t-, and Sfi21-like phages.
Related Articles
Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿
Domelier, Anne-Sophie
van der Mee-Marquet, Nathalie
Sizaret, Pierre-Yves
Héry-Arnaud, Geneviève
Lartigue, Marie-Frédérique
Mereghetti, Laurent
Quentin, Roland
Journal of Bacteriology
The application of mitomycin C induction to 114 genetically diverse Streptococcus agalactiae strains generated 36 phage suspensions. On electron microscopy of the phage suspensions, it was possible to assign the phages to the Siphoviridae family, with three different morphotypes (A, B, and C). Phage genetic diversity was evaluated by a PCR-based multilocus typing method targeting key modules located in the packaging, structural, host lysis, lysogeny, replication, and transcriptional regulation clusters and in the integrase genes and by DNA digestion with EcoRI, HindIII, and ClaI. Thirty-three phages clustering in six distantly related molecular phage groups (I to VI) were identified. Each molecular group was morphotype specific except for morphotype A phages, which were found in five of the six phage groups. The various phage groups defined on the basis of molecular group and morphotype had specific lytic activities, suggesting that each recognized particular host cell targets and had particular lytic mechanisms. Comparison of the characteristics of lysogenic and propagating strains showed no difference in the serotype or clonal complex (CC) identified by multilocus sequence typing. However, all the lysogenic CC17 and CC19 strains presented catabolic losses due to a lack of catabolic decay of dl-alpha-glycerol-phosphate substrates (CC17) and of alpha-d-glucose-1-phosphate (CC19). Moreover, the phages from CC17 lysogenic strains displayed lytic replication in bacterial hosts from all S. agalactiae phylogenetic lineages other than CC23, whereas phages obtained from non-CC17 lysogenic strains lysed bacteria of similar evolutionary origin. Our findings suggest that the adaptive evolution of S. agalactiae exposed the bacteria of this species to various phage-mediated horizontal gene transfers, which may have affected the fitness of the more virulent clones.
Related Articles
Tight Regulation of the intS Gene of the KplE1 Prophage: A New Paradigm for Integrase Gene Regulation
Panis, Gaël
Duverger, Yohann
Courvoisier-Dezord, Elise
Champ, Stéphanie
Talla, Emmanuel
Ansaldi, Mireille
PLoS Genetics
Temperate phages have the ability to maintain their genome in their host, a process called lysogeny. For most, passive replication of the phage genome relies on integration into the host's chromosome and becoming a prophage. Prophages remain silent in the absence of stress and replicate passively within their host genome. However, when stressful conditions occur, a prophage excises itself and resumes the viral cycle. Integration and excision of phage genomes are mediated by regulated site-specific recombination catalyzed by tyrosine and serine recombinases. In the KplE1 prophage, site-specific recombination is mediated by the IntS integrase and the TorI recombination directionality factor (RDF). We previously described a sub-family of temperate phages that is characterized by an unusual organization of the recombination module. Consequently, the attL recombination region overlaps with the integrase promoter, and the integrase and RDF genes do not share a common activated promoter upon lytic induction as in the lambda prophage. In this study, we show that the intS gene is tightly regulated by its own product as well as by the TorI RDF protein. In silico analysis revealed that overlap of the attL region with the integrase promoter is widely encountered in prophages present in prokaryotic genomes, suggesting a general occurrence of negatively autoregulated integrase genes. The prediction that these integrase genes are negatively autoregulated was biologically assessed by studying the regulation of several integrase genes from two different Escherichia coli strains. Our results suggest that the majority of tRNA-associated integrase genes in prokaryotic genomes could be autoregulated and that this might be correlated with the recombination efficiency as in KplE1. The consequences of this unprecedented regulation for excisive recombination are discussed.
Author Summary
Temperate bacteriophages are widespread bacterial viruses that have the ability to replicate passively in their hosts as long as no stressful conditions are encountered, a process called lysogeny. Prophage-encoded genes may benefit the host in several ways such as providing resistance to antibiotics, increased pathogenicity, or increased fitness. Most temperate phages insert their genome into the host's chromosome by site-specific recombination. After prophage induction, usually under stressful conditions, the excisive recombination constitutes a key step toward productive phage development. In this paper, we study the regulation of integrase genes that encode the enzyme required for integrative as well as excisive recombination. We noticed that for prophages inserted in or near tRNA genes the orientation of the integrase gene relative to the tRNA is crucial for its regulation.
Related Articles
Genomic Sequence and Receptor for the Vibrio cholerae Phage KSF-1Φ: Evolutionary Divergence among Filamentous Vibriophages Mediating Lateral Gene Transfer
Faruque, Shah M.
Bin Naser, Iftekhar
Fujihara, Kazutaka
Diraphat, Pornphan
Chowdhury, Nityananda
Kamruzzaman, M.
Qadri, Firdausi
Yamasaki, Shinji
Ghosh, A. N.
Mekalanos, John J.
Journal of Bacteriology
KSF-1Φ, a novel filamentous phage of Vibrio cholerae, supports morphogenesis of the RS1 satellite phage by heterologous DNA packaging and facilitates horizontal gene transfer. We analyzed the genomic sequence, morphology, and receptor for KSF-1Φ infection, as well as its phylogenetic relationships with other filamentous vibriophages. While strains carrying the mshA gene encoding mannose-sensitive hemagglutinin (MSHA) type IV pilus were susceptible to KSF-1Φ infection, naturally occurring MSHA-negative strains and an mshA deletion mutant were resistant. Furthermore, d-mannose as well as a monoclonal antibody against MSHA inhibited infection of MSHA-positive strains by the phage, suggesting that MSHA is the receptor for KSF-1Φ. The phage genome comprises 7,107 nucleotides, containing 14 open reading frames, 4 of which have predicted protein products homologous to those of other filamentous phages. Although the overall genetic organization of filamentous phages appears to be preserved in KSF-1Φ, the genomic sequence of the phage does not have a high level of identity with that of other filamentous phages and reveals a highly mosaic structure. Separate phylogenetic analysis of genomic sequences encoding putative replication proteins, receptor-binding proteins, and Zot-like proteins of 10 different filamentous vibriophages showed different results, suggesting that the evolution of these phages involved extensive horizontal exchange of genetic material. Filamentous phages which use type IV pili as receptors were found to belong to different branches. While one of these branches is represented by CTXΦ, which uses the toxin-coregulated pilus as its receptor, at least four evolutionarily diverged phages share a common receptor MSHA, and most of these phages mediate horizontal gene transfer. Since MSHA is present in a wide variety of V. cholerae strains and is presumed to express in the environment, diverse filamentous phages using this receptor are likely to contribute significantly to V. cholerae evolution.
Related Articles
Complete Genomic Sequence of SfV, a Serotype-Converting Temperate Bacteriophage of Shigella flexneri
Allison, Gwen E.
Angeles, Dario
Tran-Dinh, Nai
Verma, Naresh K.
Journal of Bacteriology
Bacteriophage SfV is a temperate serotype-converting phage of Shigella flexneri. SfV encodes the factors involved in type V O-antigen modification, and the serotype conversion and integration-excision modules of the phage have been isolated and characterized. We now report on the complete sequence of the SfV genome (37,074 bp). A total of 53 open reading frames were predicted from the nucleotide sequence, and analysis of the corresponding proteins was used to construct a functional map. The general organization of the genes in the SfV genome is similar to that of bacteriophage λ, and numerous features of the sequence are described. The superinfection immunity system of SfV includes a lambda-like repression system and a P4-like transcription termination mechanism. Sequence analysis also suggests that SfV encodes multiple DNA methylases, and experiments confirmed that orf-41 encodes a Dam methylase. Studies conducted to determine if the phage-encoded methylase confers host DNA methylation showed that the two S. flexneri strains analyzed encode their own Dam methylase. Restriction mapping and sequence analysis revealed that the phage genome has cos sites at the termini. The tail assembly and structural genes of SfV show homology to those of phage Mu and Mu-like prophages in the genome of Escherichia coli O157:H7 and Haemophilus influenzae. Significant homology (30% of the genome in total) between sections of the early, regulatory, and structural regions of the SfV genome and the e14 and KpLE1 prophages in the E. coli K-12 genome were noted, suggesting that these three phages have common evolutionary origins.
Related Articles
Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases
De Paepe, Marianne
Hutinet, Geoffrey
Son, Olivier
Amarir-Bouhram, Jihane
Schbath, Sophie
Petit, Marie-Agnès
PLoS Genetics
Bacteriophages (or phages) dominate the biosphere both numerically and in terms of genetic diversity. In particular, genomic comparisons suggest a remarkable level of horizontal gene transfer among temperate phages, favoring a high evolution rate. Molecular mechanisms of this pervasive mosaicism are mostly unknown. One hypothesis is that phage encoded recombinases are key players in these horizontal transfers, thanks to their high efficiency and low fidelity. Here, we associate two complementary in vivo assays and a bioinformatics analysis to address the role of phage encoded recombinases in genomic mosaicism. The first assay allowed determining the genetic determinants of mosaic formation between lambdoid phages and Escherichia coli prophage remnants. In the second assay, recombination was monitored between sequences on phage λ, and allowed to compare the performance of three different Rad52-like recombinases on the same substrate. We also addressed the importance of homologous recombination in phage evolution by a genomic comparison of 84 E. coli virulent and temperate phages or prophages. We demonstrate that mosaics are mainly generated by homology-driven mechanisms that tolerate high substrate divergence. We show that phage encoded Rad52-like recombinases act independently of RecA, and that they are relatively more efficient when the exchanged fragments are divergent. We also show that accessory phage genes orf and rap contribute to mosaicism. A bioinformatics analysis strengthens our experimental results by showing that homologous recombination left traces in temperate phage genomes at the borders of recently exchanged fragments. We found no evidence of exchanges between virulent and temperate phages of E. coli. Altogether, our results demonstrate that Rad52-like recombinases promote gene shuffling among temperate phages, accelerating their evolution. This mechanism may prove to be more general, as other mobile genetic elements such as ICE encode Rad52-like functions, and play an important role in bacterial evolution itself.
Author Summary
Temperate bacteriophages (or phages) are bacterial viruses that, unlike virulent phages, have the ability to enter a prophage dormant state upon infection, in which they stably replicate with the bacterial genome. A majority of bacterial genomes contain multiple active or defective prophages, and numerous bacterial phenotypes are modified by these prophages, such as increased virulence. These mobile genetic elements are subject to high levels of genetic exchanges, through which new genes are constantly imported into bacterial genomes. Phage-encoded homologous recombination enzymes, or recombinases, are potentially key actors in phage genome shuffling. In this work, we show that gene acquisition in temperate phages is strongly dependent on the presence of sequence homology, but is highly tolerant to divergence. We report that gene exchanges are mainly catalyzed by recombinases found on temperate phages, and show that four different Rad52-like recombinases have a relaxed fidelity in vivo, compared to RecA. This high capacity of exchange speeds up evolution of phages, and indirectly also the evolution of bacteria.
Related Articles
Characterization of a Shiga Toxin-Encoding Temperate Bacteriophage of Shigella sonnei
Strauch, Eckhard
Lurz, Rudi
Beutin, Lothar
Infection and Immunity
A Shiga toxin (Stx)-encoding temperate bacteriophage of Shigella sonnei strain CB7888 was investigated for its morphology, DNA similarity, host range, and lysogenization in Shigella and Escherichia coli strains. Phage 7888 formed plaques on a broad spectrum of Shigella strains belonging to different species and serotypes, including Stx-producing Shigella dysenteriae type 1. With E. coli, only strains with rough lipopolysaccharide were sensitive to this phage. The phage integrated into the genome of nontoxigenic S. sonnei and laboratory E. coli K-12 strains, which became Stx positive upon lysogenization. Moreover, phage 7888 is capable of transducing chromosomal genes in E. coli K-12. The relationships of phage 7888 with the E. coli Stx1-producing phage H-19B and the E. coli Stx2-producing phage 933W were investigated by DNA cross-hybridization of phage genomes and by nucleotide sequencing of an 8,053-bp DNA region of the phage 7888 genome flanking the stx genes. By these methods, a high similarity was found between phages 7888 and 933W. Much less similarity was found between phages H-19B and 7888. As in the other Stx phages, a regulatory region involved in Q-dependent expression is found upstream of stxA and stxB (stx gene) in phage 7888. The morphology of phage 7888 was similar to that of phage 933W, which shows a hexagonal head and a short tail. Our findings demonstrate that stx genes are naturally transferable and are expressed in strains of S. sonnei, which points to the continuous evolution of human-pathogenic Shigella by horizontal gene transfer.
Related Articles
Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages
Merrill, Bryan D
Grose, Julianne H
Breakwell, Donald P
Burnett, Sandra H
BMC Genomics
Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report includes an in-depth analysis of the structure, genomes, and relatedness of P. larvae myoviruses Abouo, Davis, Emery, Jimmer1, Jimmer2, and siphovirus phiIBB_Pl23 to each other and to other known phages.
P. larvae phages Abouo, Davies, Emery, Jimmer1, and Jimmer2 are myoviruses with ~50 kbp genomes. The six P. larvae phages form three distinct groups by dotplot analysis. An annotated linear genome map of these six phages displays important identifiable genes and demonstrates the relationship between phages. Sixty phage assembly or structural protein genes and 133 regulatory or other non-structural protein genes were identifiable among the six P. larvae phages. Jimmer1, Jimmer2, and Davies formed stable lysogens resistant to superinfection by genetically similar phages. The correlation between tape measure protein gene length and phage tail length allowed identification of co-isolated phages Emery and Abouo in electron micrographs. A Phamerator database was assembled with the P. larvae phage genomes and 107 genomes of Firmicute-infecting phages, including 71 Bacillus phages. Phamerator identified conserved domains in 1,501 of 6,181 phamilies (only 24.3%) encoded by genes in the database and revealed that P. larvae phage genomes shared at least one phamily with 72 of the 107 other phages. The phamily relationship of large terminase proteins was used to indicate putative DNA packaging strategies. Analyses from CoreGenes, Phamerator, and electron micrograph measurements indicated Jimmer1, Jimmer2, Abouo and Davies were related to phages phiC2, EJ-1, KC5a, and AQ113, which are small-genome myoviruses that infect Streptococcus, Lactobacillus, and Clostridium, respectively.
This paper represents the first comparison of phage genomes in the Paenibacillus genus and the first organization of P. larvae phages based on sequence and structure. This analysis provides an important contribution to the field of bacteriophage genomics by serving as a foundation on which to build an understanding of the natural predators of P. larvae.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-745) contains supplementary material, which is available to authorized users.
Paenibacillus larvae; Bacteriophage; Jimmer1; Jimmer2; Emery; Abouo; Davies; phiIBB_Pl23; Phamerator; Phage genomics
Related Articles
Genome classification by gene distribution: An overlapping subspace clustering approach
Li, Jason
Halgamuge, Saman K
Tang, Sen-Lin
BMC Evolutionary Biology
Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent approach that addresses this problem is the unsupervised clustering of genomes based on gene order and genome position, which helps to reveal species relationships that may not be apparent from traditional phylogenetic methods.
We propose the use of an overlapping subspace clustering algorithm for such genome classification problems. The advantage of subspace clustering over traditional clustering is that it can associate clusters with gene arrangement patterns, preserving genomic information in the clusters produced. Additionally, overlapping capability is desirable for the discovery of multiple conserved patterns within a single genome, such as those acquired from different species via horizontal gene transfers. The proposed method involves a novel strategy to vectorize genomes based on their gene distribution. A number of existing subspace clustering and biclustering algorithms were evaluated to identify the best framework upon which to develop our algorithm; we extended a generic subspace clustering algorithm called HARP to incorporate overlapping capability. The proposed algorithm was assessed and applied on bacteriophage genomes. The phage grouping results are consistent overall with the Phage Proteomic Tree and showed common genomic characteristics among the TP901-like, Sfi21-like and sk1-like phage groups. Among 441 phage genomes, we identified four significantly conserved distribution patterns structured by the terminase, portal, integrase, holin and lysin genes. We also observed a subgroup of Sfi21-like phages comprising a distinctive divergent genome organization and identified nine new phage members to the Sfi21-like genus: Staphylococcus 71, phiPVL108, Listeria A118, 2389, Lactobacillus phi AT3, A2, Clostridium phi3626, Geobacillus GBSV1, and Listeria monocytogenes PSA.
The method described in this paper can assist evolutionary study through objectively classifying genomes based on their resemblance in gene order, gene content and gene positions. The method is suitable for application to genomes with high genetic exchange and various conserved gene arrangement, as demonstrated through our application on phages.
Related Articles
Genomic analysis of bacteriophage ε34 of Salmonella enterica serovar Anatum (15+)
Villafane, Robert
Zayas, Milka
Gilcrease, Eddie B
Kropinski, Andrew M
Casjens, Sherwood R
BMC Microbiology
The presence of prophages has been an important variable in genetic exchange and divergence in most bacteria. This study reports the determination of the genomic sequence of Salmonella phage ε34, a temperate bacteriophage that was important in the early study of prophages that modify their hosts' cell surface and is of a type (P22-like) that is common in Salmonella genomes.
The sequence shows that ε34 is a mosaically related member of the P22 branch of the lambdoid phages. Its sequence is compared with the known P22-like phages and several related but previously unanalyzed prophage sequences in reported bacterial genome sequences.
These comparisons indicate that there has been little if any genetic exchange within the procapsid assembly gene cluster with P22-like E. coli/Shigella phages that are have orthologous but divergent genes in this region. Presumably this observation reflects the fact that virion assembly proteins interact intimately and divergent proteins can no longer interact. On the other hand, non-assembly genes in the "ant moron" appear to be in a state of rapid flux, and regulatory genes outside the assembly gene cluster have clearly enjoyed numerous and recent horizontal exchanges with phages outside the P22-like group. The present analysis also shows that ε34 harbors a gtrABC gene cluster which should encode the enzymatic machinery to chemically modify the host O antigen polysaccharide, thus explaining its ability to alter its host's serotype. A comprehensive comparative analysis of the known phage gtrABC gene clusters shows that they are highly mobile, having been exchanged even between phage types, and that most "bacterial" gtrABC genes lie in prophages that vary from being largely intact to highly degraded. Clearly, temperate phages are very major contributors to the O-antigen serotype of their Salmonella hosts.
Related Articles
Four Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages
Niu, Yan D.
McAllister, Tim A.
Nash, John H. E.
Kropinski, Andrew M.
Stanford, Kim
PLoS ONE
The T1-like bacteriophages vB_EcoS_AHP24, AHS24, AHP42 and AKS96 of the family Siphoviridae were shown to lyse common phage types of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157:H7), but not non-O157 E. coli. All contained circularly permuted genomes of 45.7–46.8 kb (43.8–44 mol% G+C) encoding 74–81 open reading frames and 1 arginyl-tRNA. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the structural proteins were identical among the four phages. Further proteomic analysis identified seven structural proteins responsible for tail fiber, tail tape measure protein, major capsid, portal protein as well as major and minor tail proteins. Bioinformatic analyses on the proteins revealed that genomes of AHP24, AHS24, AHP42 and AKS96 did not encode for bacterial virulence factors, integration-related proteins or antibiotic resistance determinants. All four phages were highly lytic to STEC O157:H7 with considerable potential as biocontrol agents. Comparative genomic, proteomic and phylogenetic analysis suggested that the four phages along with 17 T1-like phage genomes from database of National Center for Biotechnology Information (NCBI) can be assigned into a proposed subfamily "Tunavirinae" with further classification into five genera, namely "Tlslikevirus" (TLS, FSL SP-126), "Kp36likevirus" (KP36, F20), Tunalikevirus (T1, ADB-2 and Shf1), "Rtplikevirus" (RTP, vB_EcoS_ACG-M12) and "Jk06likevirus" (JK06, vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96, phiJLA23, phiKP26, phiEB49). The fact that the viruses related to JK06 have been isolated independently in Israel (JK06) (GenBank Assession #, NC_007291), Canada (vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96) and Mexico (phiKP26, phiJLA23) (between 2005 and 2011) indicates that these similar phages are widely distributed, and that horizontal gene transfer does not always prevent the characterization of bacteriophage evolution. With this new scheme, any new discovered phages with same type can be more properly identified. Genomic- and proteomic- based taxonomic classification of phages would facilitate better understanding phages diversity and genetic traits involved in phage evolution.
Related Articles
Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica.
Wang, F S
Whittam, T S
Selander, R K
Journal of Bacteriology
Sequences of the icd gene, encoding isocitrate dehydrogenase (IDH), were obtained for 33 strains representing the major phylogenetic lineages of Escherichia coli and Salmonella enterica. Evolutionary relationships of the strains based on variation in icd are generally similar to those previously obtained for several other housekeeping and for invasion genes, but the sequences of S. enterica subspecies V strains are unusual in being almost intermediate between those of the other S. enterica subspecies and E. coli. For S. enterica, the ratio of synonymous (silent) to nonsynonymous (replacement) nucleotide substitutions between pairs of strains was larger than comparable values for 12 other housekeeping and invasion genes, reflecting unusually strong purifying selection against amino acid replacement in the IDH enzyme. All amino acids involved in the catalytic activity and conformational changes of IDH are strictly conserved within and between species. In E. coli, the level of variation at the 3' end of the gene is elevated by the presence in some strains of a 165-bp replacement sequence supplied by the integration of either lambdoid phage 21 or defective prophage element e14. The 72 members of the E. coli Reference Collection (ECOR) and five additional E. coli strains were surveyed for the presence of phage 21 (as prophage) by PCR amplification of a phage 21-specific fragment in and adjacent to the host icd, and the sequence of the phage 21 segment extending from the 3' end of icd through the integrase gene (int) was determined in nine strains of E. coli. Phage 21 was found in 39% of E. coli strains, and its distribution among the ECOR strains is nonrandom. In two ECOR strains, the phage 21 int gene is interrupted by a 1,313-bp insertion element that has 99.3% nucleotide sequence identity with IS3411 of E. coli. The phylogenetic relationships of phage 21 strains derived from sequences of two different genomic regions were strongly incongruent, providing evidence of frequent recombination.
Related Articles
Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts
Sullivan, Matthew B
Lindell, Debbie
Lee, Jessica A
Thompson, Luke R
Bielawski, Joseph P
Chisholm, Sallie W
PLoS Biology
Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and evolutionary dynamics of this phenomenon, 33 cultured cyanophages of known family and host range and viral DNA from field samples were screened for the presence of two core photosystem reaction center genes, psbA and psbD. Combining this expanded dataset with published data for nine other cyanophages, we found that 88% of the phage genomes contain psbA, and 50% contain both psbA and psbD. The psbA gene was found in all myoviruses and Prochlorococcus podoviruses, but could not be amplified from Prochlorococcus siphoviruses or Synechococcus podoviruses. Nearly all of the phages that encoded both psbA and psbD had broad host ranges. We speculate that the presence or absence of psbA in a phage genome may be determined by the length of the latent period of infection. Whether it also carries psbD may reflect constraints on coupling of viral- and host-encoded PsbA–PsbD in the photosynthetic reaction center across divergent hosts. Phylogenetic clustering patterns of these genes from cultured phages suggest that whole genes have been transferred from host to phage in a discrete number of events over the course of evolution (four for psbA, and two for psbD), followed by horizontal and vertical transfer between cyanophages. Clustering patterns of psbA and psbD from Synechococcus cells were inconsistent with other molecular phylogenetic markers, suggesting genetic exchanges involving Synechococcus lineages. Signatures of intragenic recombination, detected within the cyanophage gene pool as well as between hosts and phages in both directions, support this hypothesis. The analysis of cyanophage psbA and psbD genes from field populations revealed significant sequence diversity, much of which is represented in our cultured isolates. Collectively, these findings show that photosynthesis genes are common in cyanophages and that significant genetic exchanges occur from host to phage, phage to host, and within the phage gene pool. This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution.
Analysis of 33 cultured cyanophages of known family and host range, as well as viral DNA from field samples, reveals the prevalence of photosynthesis genes in cyanophages and demonstrates significant genetic exchanges between host and phage.
Related Articles
Bacteriophage 2851 Is a Prototype Phage for Dissemination of the Shiga Toxin Variant Gene 2c in Escherichia coli O157:H7▿ †
Strauch, Eckhard
Hammerl, Jens Andre
Konietzny, Antje
Schneiker-Bekel, Susanne
Arnold, Walter
Goesmann, Alexander
Pühler, Alfred
Beutin, Lothar
Infection and Immunity
The production of Shiga toxin (Stx) (verocytotoxin) is a major virulence factor of Escherichia coli O157:H7 strains (Shiga toxin-producing E. coli [STEC] O157). Two types of Shiga toxins, designated Stx1 and Stx2, are produced in STEC O157. Variants of the Stx2 type (Stx2, Stx2c) are associated with high virulences of these strains for humans. A bacteriophage designated 2851 from a human STEC O157 encoding the Stx2c variant was described previously. Nucleotide sequence analysis of the phage 2851 genome revealed 75 predicted coding sequences and indicated a mosaic structure typical for lambdoid phages. Analyses of free phages and K-12 phage 2851 lysogens revealed that upon excision from the bacterial chromosome, the loss of a phage-encoded IS629 element leads to fusion of phage antA and antB genes, with the generation of a recombined antAB gene encoding a strong antirepressor. In wild-type E. coli O157 as well as in K-12 strains, phage 2851 was found to be integrated in the sbcB locus. Additionally, phage 2851 carries an open reading frame which encodes an OspB-like type III effector similar to that found in Shigella spp. Investigation of 39 stx2c E. coli O157 strains revealed that all except 1 were positive for most phage 2851-specific genes and possessed a prophage with the same border sequences integrated into the sbcB locus. Phage 2851-specific sequences were absent from most stx2c-negative E. coli O157 strains, and we suggest that phage 2851-like phages contributed significantly to the dissemination of the Stx2c variant toxin within this group of E. coli.
Related Articles
Analysis of the Genetic Switch and Replication Region of a P335-Type Bacteriophage with an Obligate Lytic Lifestyle on Lactococcus lactis†
Madsen, Søren M.
Mills, David
Djordjevic, Gordana
Israelsen, Hans
Klaenhammer, Todd R.
Applied and Environmental Microbiology
The DNA sequence of the replication module, part of the lysis module, and remnants of a lysogenic module from the lytic P335 species lactococcal bacteriophage φ31 was determined, and its regulatory elements were investigated. The identification of a characteristic genetic switch including two divergent promoters and two cognate repressor genes strongly indicates that φ31 was derived from a temperate bacteriophage. Regulation of the two early promoters was analyzed by primer extension and transcriptional promoter fusions to a lacLM reporter. The regulatory behavior of the promoter region differed significantly from the genetic responses of temperate Lactococcus lactis phages. The cro gene homologue regulates its own production and is an efficient repressor of cI gene expression. No detectable cI gene expression could be measured in the presence of cro. cI gene expression in the absence of cro exerted minor influences on the regulation of the two promoters within the genetic switch. Homology comparisons revealed a replication module which is most likely expressed from the promoter located upstream of the cro gene homologue. The replication module encoded genes with strong homology to helicases and primases found in several Streptococcus thermophilus phages. Downstream of the primase homologue, an AT-rich noncoding origin region was identified. The characteristics and location of this region and its ability to reduce the efficiency of plaquing of φ31 106-fold when present at high copy number in trans provide evidence for identification of the phage origin of replication. Phage φ31 is an obligately lytic phage that was isolated from commercial dairy fermentation environments. Neither a phage attachment site nor an integrase gene, required to establish lysogeny, was identified, explaining its lytic lifestyle and suggesting its origin from a temperate phage ancestor. Several regions showing extensive DNA and protein homologies to different temperate phages of Lactococcus, Lactobacillus, and Streptococcus were also discovered, indicating the likely exchange of DNA cassettes through horizontal gene transfer in the dynamic ecological environment of dairy fermentations.
Related Articles
The Tripartite Associations between Bacteriophage, Wolbachia, and Arthropods
Bordenstein, Seth R
Marshall, Michelle L
Fry, Adam J
Kim, Ulandt
Wernegreen, Jennifer J
PLoS Pathogens
By manipulating arthropod reproduction worldwide, the heritable endosymbiont Wolbachia has spread to pandemic levels. Little is known about the microbial basis of cytoplasmic incompatibility (CI) except that bacterial densities and percentages of infected sperm cysts associate with incompatibility strength. The recent discovery of a temperate bacteriophage (WO-B) of Wolbachia containing ankyrin-encoding genes and virulence factors has led to intensifying debate that bacteriophage WO-B induces CI. However, current hypotheses have not considered the separate roles that lytic and lysogenic phage might have on bacterial fitness and phenotype. Here we describe a set of quantitative approaches to characterize phage densities and its associations with bacterial densities and CI. We enumerated genome copy number of phage WO-B and Wolbachia and CI penetrance in supergroup A- and B-infected males of the parasitoid wasp Nasonia vitripennis. We report several findings: (1) variability in CI strength for A-infected males is positively associated with bacterial densities, as expected under the bacterial density model of CI, (2) phage and bacterial densities have a significant inverse association, as expected for an active lytic infection, and (3) CI strength and phage densities are inversely related in A-infected males; similarly, males expressing incomplete CI have significantly higher phage densities than males expressing complete CI. Ultrastructural analyses indicate that approximately 12% of the A Wolbachia have phage particles, and aggregations of these particles can putatively occur outside the Wolbachia cell. Physical interactions were observed between approximately 16% of the Wolbachia cells and spermatid tails. The results support a low to moderate frequency of lytic development in Wolbachia and an overall negative density relationship between bacteriophage and Wolbachia. The findings motivate a novel phage density model of CI in which lytic phage repress Wolbachia densities and therefore reproductive parasitism. We conclude that phage, Wolbachia, and arthropods form a tripartite symbiotic association in which all three are integral to understanding the biology of this widespread endosymbiosis. Clarifying the roles of lytic and lysogenic phage development in Wolbachia biology will effectively structure inquiries into this research topic.
Symbiotic bacteria that are maternally inherited are widespread in terrestrial invertebrates. Such bacteria infect the cells of reproductive tissues and can have important evolutionary and developmental effects on the host. Often these inherited symbionts develop beneficial relationships with their hosts, but some species can also selfishly alter invertebrate reproduction to increase the numbers of infected females (the transmitting sex of the bacteria) in the population. Bacterial-mediated distortions such as male-killing, feminization, parthenogenesis induction, and cytoplasmic incompatibility are collectively known as "reproductive parasitism." In this article, the investigators show that the associations between the most common reproductive parasite in the biosphere (Wolbachia) and a parasitic wasp host are affected by a mobile element—a temperate bacteriophage of Wolbachia. In contrast to recent reports that suggest bacteriophage WO-B may induce reproductive parasitism, the authors' quantitative and ultrastructural analyses indicate that lytic phage WO-B are lethal and therefore associate with a reduction in both Wolbachia densities and reproductive parasitism. Based on these data, the authors propose a phage density model in which lytic phage development specifically leads to a reduction, rather than induction, of reproductive parisitism. The study is among the first investigations to show that lytic bacteriophage inversely associate with the densities and phenotype of an obligate intracellular bacterium.
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Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes
Swanson, Maud M.
Reavy, Brian
Makarova, Kira S.
Cock, Peter J.
Hopkins, David W.
Torrance, Lesley
Koonin, Eugene V.
Taliansky, Michael
PLoS ONE
A novel bacteriophage infecting Staphylococus pasteuri was isolated during a screen for phages in Antarctic soils. The phage named SpaA1 is morphologically similar to phages of the family Siphoviridae. The 42,784 bp genome of SpaA1 is a linear, double-stranded DNA molecule with 3′ protruding cohesive ends. The SpaA1 genome encompasses 63 predicted protein-coding genes which cluster within three regions of the genome, each of apparently different origin, in a mosaic pattern. In two of these regions, the gene sets resemble those in prophages of Bacillus thuringiensis kurstaki str. T03a001 (genes involved in DNA replication/transcription, cell entry and exit) and B. cereus AH676 (additional regulatory and recombination genes), respectively. The third region represents an almost complete genome (except for the short terminal segments) of a distinct bacteriophage, MZTP02. Nearly the same gene module was identified in prophages of B. thuringiensis serovar monterrey BGSC 4AJ1 and B. cereus Rock4-2. These findings suggest that MZTP02 can be shuttled between genomes of other bacteriophages and prophages, leading to the formation of chimeric genomes. The presence of a complete phage genome in the genome of other phages apparently has not been described previously and might represent a 'fast track' route of virus evolution and horizontal gene transfer. Another phage (BceA1) nearly identical in sequence to SpaA1, and also including the almost complete MZTP02 genome within its own genome, was isolated from a bacterium of the B. cereus/B. thuringiensis group. Remarkably, both SpaA1 and BceA1 phages can infect B. cereus and B. thuringiensis, but only one of them, SpaA1, can infect S. pasteuri. This finding is best compatible with a scenario in which MZTP02 was originally contained in BceA1 infecting Bacillus spp, the common hosts for these two phages, followed by emergence of SpaA1 infecting S. pasteuri.
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First genome sequences of Achromobacter phages reveal new members of the N4 family
Wittmann, Johannes
Dreiseikelmann, Brigitte
Rohde, Manfred
Meier-Kolthoff, Jan P
Bunk, Boyke
Rohde, Christine
Virology Journal
Multi-resistant Achromobacter xylosoxidans has been recognized as an emerging pathogen causing nosocomially acquired infections during the last years. Phages as natural opponents could be an alternative to fight such infections. Bacteriophages against this opportunistic pathogen were isolated in a recent study. This study shows a molecular analysis of two podoviruses and reveals first insights into the genomic structure of Achromobacter phages so far.
Growth curve experiments and adsorption kinetics were performed for both phages. Adsorption and propagation in cells were visualized by electron microscopy. Both phage genomes were sequenced with the PacBio RS II system based on single molecule, real-time (SMRT) technology and annotated with several bioinformatic tools. To further elucidate the evolutionary relationships between the phage genomes, a phylogenomic analysis was conducted using the genome Blast Distance Phylogeny approach (GBDP).
In this study, we present the first detailed analysis of genome sequences of two Achromobacter phages so far. Phages JWAlpha and JWDelta were isolated from two different waste water treatment plants in Germany. Both phages belong to the Podoviridae and contain linear, double-stranded DNA with a length of 72329 bp and 73659 bp, respectively. 92 and 89 putative open reading frames were identified for JWAlpha and JWDelta, respectively, by bioinformatic analysis with several tools. The genomes have nearly the same organization and could be divided into different clusters for transcription, replication, host interaction, head and tail structure and lysis. Detailed annotation via protein comparisons with BLASTP revealed strong similarities to N4-like phages.
Analysis of the genomes of Achromobacter phages JWAlpha and JWDelta and comparisons of different gene clusters with other phages revealed that they might be strongly related to other N4-like phages, especially of the Escherichia group. Although all these phages show a highly conserved genomic structure and partially strong similarities at the amino acid level, some differences could be identified. Those differences, e.g. the existence of specific genes for replication or host interaction in some N4-like phages, seem to be interesting targets for further examination of function and specific mechanisms, which might enlighten the mechanism of phage establishment in the host cell after infection.
Achromobacter xylosoxidans; N4-like phage; Genome; Lar-like protein; N4likevirus; Podoviridae; GBDP
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Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability
Bobay, Louis-Marie
Touchon, Marie
Rocha, Eduardo P. C.
PLoS Genetics
Phages, like many parasites, tend to have small genomes and may encode autonomous functions or manipulate those of their hosts'. Recombination functions are essential for phage replication and diversification. They are also nearly ubiquitous in bacteria. The E. coli genome encodes many copies of an octamer (Chi) motif that upon recognition by RecBCD favors repair of double strand breaks by homologous recombination. This might allow self from non-self discrimination because RecBCD degrades DNA lacking Chi. Bacteriophage Lambda, an E. coli parasite, lacks Chi motifs, but escapes degradation by inhibiting RecBCD and encoding its own autonomous recombination machinery. We found that only half of 275 lambdoid genomes encode recombinases, the remaining relying on the host's machinery. Unexpectedly, we found that some lambdoid phages contain extremely high numbers of Chi motifs concentrated between the phage origin of replication and the packaging site. This suggests a tight association between replication, packaging and RecBCD-mediated recombination in these phages. Indeed, phages lacking recombinases strongly over-represent Chi motifs. Conversely, phages encoding recombinases and inhibiting host recombination machinery select for the absence of Chi motifs. Host and phage recombinases use different mechanisms and the latter are more tolerant to sequence divergence. Accordingly, we show that phages encoding their own recombination machinery have more mosaic genomes resulting from recent recombination events and have more diverse gene repertoires, i.e. larger pan genomes. We discuss the costs and benefits of superseding or manipulating host recombination functions and how this decision shapes phage genome structure and evolvability.
Author Summary
Bacterial viruses, called bacteriophages, are extremely abundant in the biosphere. They have key roles in the regulation of bacterial populations and in the diversification of bacterial genomes. Among these viruses, lambdoid phages are very abundant in enterobacteria and exchange genetic material very frequently. This latter process is thought to increase phage diversity and therefore facilitate adaptation to hosts. Recombination is also essential for the replication of many lambdoid phages. Lambdoids have been described to encode their own recombination genes and inhibit their hosts'. In this study, we show that lambdoids are split regarding their capacity to encode autonomous recombination functions and that this affects the abundance of recombination-related sequence motifs. Half of the phages encode an autonomous system and inhibit their hosts'. The trade-off between superseding and manipulating the hosts' recombination functions has important consequences. The phages encoding autonomous recombination functions have more diverse gene repertoires and recombine more frequently. Viruses, as many other parasites, have small genomes and depend on their hosts for several housekeeping functions. Hence, they often face trade-offs between supersession and manipulation of molecular machineries. Our results suggest these trade-offs may shape viral gene repertoires, their sequence composition and even influence their evolvability.
Related Articles
Genome organisation of the Acinetobacter lytic phage ZZ1 and comparison with other T4-like Acinetobacter phages
Jin, Jing
Li, Zhen-Jiang
Wang, Shu-Wei
Wang, Shan-Mei
Chen, Song-Jian
Huang, De-Hai
Zhang, Gai
Li, Ya-Hui
Wang, Xiao-Ting
Wang, Jin
Zhao, Guo-Qiang
BMC Genomics
Phage ZZ1, which efficiently infects pathogenic Acinetobacter baumannii strains, is the fifth completely sequenced T4-like Acinetobacter phage to date. To gain a better understanding of the genetic characteristics of ZZ1, bioinformatics and comparative genomic analyses of the T4 phages were performed.
The 166,687-bp double-stranded DNA genome of ZZ1 has the lowest GC content (34.4%) of the sequenced T4-like Acinetobacter phages. A total of 256 protein-coding genes and 8 tRNA genes were predicted. Forty-three percent of the predicted ZZ1 proteins share up to 73% amino acid identity with T4 proteins, and the homologous genes generally retained the same order and transcriptional direction. Beyond the conserved structural and DNA replication modules, T4 and ZZ1 have diverged substantially by the acquisition and deletion of large blocks of unrelated genes, especially in the first halves of their genomes. In addition, ZZ1 and the four other T4-like Acinetobacter phage genomes (Acj9, Acj61, 133, and Ac42) share a well-organised and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. Of the ZZ1 proteins, 70, 64, 61, and 56% share up to 86, 85, 81, and 83% amino acid identity with Acj9, Acj61, 133, and Ac42 proteins, respectively. ZZ1 has a different number and types of tRNAs than the other 4 Acinetobacter phages, although some of the ZZ1-encoded tRNAs share high sequence similarity with the tRNAs from these phages. Over half of ZZ1-encoded tRNAs (5 out of 8) are related to optimal codon usage for ZZ1 proteins. However, this correlation was not present in any of the other 4 Acinetobacter phages.
The comparative genomic analysis of these phages provided some new insights into the evolution and diversity of Acinetobacter phages, which might elucidate the evolutionary origin and host-specific adaptation of these phages.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-793) contains supplementary material, which is available to authorized users.
Phage genome annotation; Phage genome organisation; Comparative genomic analyses; T4-like phage
Related Articles
Vibrio vulnificus Phage PV94 Is Closely Related to Temperate Phages of V. cholerae and Other Vibrio Species
Pryshliak, Mark
Hammerl, Jens A.
Reetz, Jochen
Strauch, Eckhard
Hertwig, Stefan
PLoS ONE
Vibrio vulnificus is an important pathogen which can cause serious infections in humans. Yet, there is limited knowledge on its virulence factors and the question whether temperate phages might be involved in pathogenicity, as is the case with V. cholerae. Thus far, only two phages (SSP002 and VvAW1) infecting V. vulnificus have been genetically characterized. These phages were isolated from the environment and are not related to Vibrio cholerae phages. The lack of information on temperate V. vulnificus phages prompted us to isolate those phages from lysogenic strains and to compare them with phages of other Vibrio species.
In this study the temperate phage PV94 was isolated from a V. vulnificus biotype 1 strain by mitomycin C induction. PV94 is a myovirus whose genome is a linear double-stranded DNA of 33,828 bp with 5′-protruding ends. Sequence analysis of PV94 revealed a modular organization of the genome. The left half of the genome comprising the immunity region and genes for the integrase, terminase and replication proteins shows similarites to V. cholerae kappa phages whereas the right half containing genes for structural proteins is closely related to a prophage residing in V. furnissii NCTC 11218.
We present the first genomic sequence of a temperate phage isolated from a human V. vulnificus isolate. The sequence analysis of the PV94 genome demonstrates the wide distribution of closely related prophages in various Vibrio species. Moreover, the mosaicism of the PV94 genome indicates a high degree of horizontal genetic exchange within the genus Vibrio, by which V. vulnificus might acquire virulence-associated genes from other species.
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Chances are your team is pleased with your managerial style.
Sep 01, 2008
They really, really like you: Eighty-three percent of team members said so. Two-thirds said that if they were in charge of hiring, they'd hire their boss. And 43 percent would follow their boss to another practice. According to respondents, the top five traits of these much-loved managers were fairness, an even temper, good listening skills, thoughtfulness, and a cheerful attitude.
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Acquirers stepped up their activity in the Internet of Things (IoT) marketplace in 2014, spending approximately $14.3bn to acquire 60 companies in 2014 according to 451 Research. That spending is almost eight times the total spent by acquirers prior to 2014 and represents a fortyfold increase over 2013.
The number of deals increased more than twofold as companies such as Google, Samsung, Cisco, Intel, PTC, Qualcomm and many others staked out their ground in an effort to position IoT as a key contributor to corporate strategy. 451 Research tracks IoT and wearable tech deal activity via its proprietary database, the 451 M&A KnowledgeBase, which has recorded more than 40,000 technology merger and acquisition transactions since 2002.
The sharp rise in deal-making activity in 2014 suggests that market forces surrounding IoT have become sufficiently compelling to demand action. "Acquirers don't want to cede anything to a growing list of competitors as demand for IoT services in both consumer and industrial markets builds," said Brian Partridge, Vice President of 451 Research's mobility team.
"The expected growth in this segment will drive enterprise spending across a myriad of building-block categories from embedded computing systems to communication infrastructure, IP networking, cloud and datacenter technologies that will form the foundation of the next generation of connected machines and services. We expect to see even more activity in 2015 as the cost and risk hurdles to IoT adoption are overcome and the competition to serve these markets increases. Any firm with the strategic intention of being an IT infrastructure and services leader over the next 10 years does not have the option to ignore this market," Partridge added.
M&A activity in 2014 was almost evenly split between IoT-enabling horizontal infrastructure and vertical applications. In the infrastructure arena, acquirers notched 20 deals, primarily targeting a broad range of sensors, semiconductors, software platforms, security infrastructure and connectivity technologies needed for IoT to work effectively. Within the verticals, the transport and logistics segment led the field with 11 transactions, followed by the fitness and healthcare segment with 10 transactions. Acquirers also purchased five companies related to the home automation segment.
Key transactions identified by the 451 Research mobility team for the year include:
Home Automation and Control:
– Google acquired Nest Labs for $3.2bn in January.
– Nest Labs acquired Dropcam for $555m in June.
These deals were significant due to their size, revenue multiples, market valuation and the brands behind the transactions. Google and Samsung view the connected home as logical extensions from their respective positions of strength in smart devices and operating systems.
IoT-Enabling Platforms:
– PTC acquired Axeda for $170m in August.
This deal provides a lens into the changing competitive dynamics for making products smart. PCT's IoT acquisition spree lines it up as a competitor to more traditional enterprise IT software players such as SAP, IBM and Oracle.
Wearable Technology:
– Intel acquired BASIS Science for $100m in March.
Intel continued to build on its quest to become a dominant supplier in key parts of the value stack for IoT in both consumer and industrial segments. BASIS was somewhat of a surprise acquisition for the chipmaker because it was selling its wearable fitness trackers directly to consumers while competing with companies such as Jawbone and Fitbit.
Topics: Internet of Things


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Updated 05/08/2015
On the outside, it feels like Spanish Colonial; on the inside, this 12-story hotel, built in 1926, is a mix of Mexican, Mediterranean, and Moroccan styles, with earth tones, hand-glazed walls, and wrought-iron beds. You can lounge around the pool and bubbling hot tub surrounded by tropical greenery under the shadow of downtown skyscrapers—make it even better with a soothing drink from the back patio bar.
939 S. Figueroa St., Los Angeles, California, 90015, United States
213-627–8971; 800-421–9092
Website: www.figueroahotel.com
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Problem Sleuth is the third MS Paint Adventure. Initially a parody of detective noir stories, though quickly abandoning that premise in favor of stranger and wackier plot directions, the adventure tells the story of Problem Sleuth, Ace Dick and Pickle Inspector, three competing private detectives who operate out of neighboring offices in the same building. When all three become trapped inside their respective offices, they join forces to find a way out of their predicament and defeat the evil Mobster Kingpin, who possesses the key they need to leave their building.
Problem Sleuth debuted on March 10, 2008, relaunching MS Paint Adventures after the abandonment of Bard Quest eight months earlier caused the site to be shut down indefinitely. Exactly one year later, on March 10, 2009, the central storyline reached its conclusion, and, after the release of an additional epilogue chapter, Problem Sleuth ended on April 7 with a total of 1,673 pages.
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We've hit our second update break! We'll get to see what happens next when it's the fifteenth in a European country.
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Hussie has confirmed on Twitter that edits of Star Trek: The Next Generation are returning after almost five years!
With today's update, we've hit the first week-long break in the horse calendars. Your F5-pressing finger can take a vacation until it's the 25th in some European country in a little over a week.
Helping out


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Events CorpGov.net publisher James McRitchie will attend:
2015 Public Funds Forum, Montage Resort, Laguna Beach, CA, 9/8-10. Register for the event.
ICGN Boston Event – 29-30 September, Westin Copley Plaza in Boston, MA. Register. Notes from the 2013 ICGN in New York
CII's 2015 fall conference. Event will take place from Wednesday, September 30 to Friday, October 2 at the Westin Copley Plaza in Boston, MA. Register for the event. Notes from the Fall 2014 CII Conference.
NYSE's 12th Annual Boardroom Summit, NYC, 10/12-14/2015, Grand Hyatt. I'll be on the Shareholder Activism panel. Register.
All in for Impact, 2015 SRI Conference on Sustainable, Responsible, Impact Investing!, 11/3-5, the Broadmoor, Colorado Springs. Register for the event.
Events CorpGov.net publisher James McRitchie will attend:


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Positive Women
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Save The Date!!!!
Lord Teach Me To Pray
Annual Weekend of Prayer 2016
March 10-March 13, 2016
Airport Hilton Hotel, New Orleans, Louisiana
Scriptural Theme for Weekend to be Chosen Soon!
The weekend begins Thursday evening March 10, 2016 with 7:00 PM Opening Mass with Bishop Fernand Cheri, of the Archdiocese of New Orleans. A reception follows.
This is truly a Weekend of Prayer! Mass each day, Confessions, Adoration, Holy Hours! "It is like stepping into Heaven for the weekend!" (quote from past participant).
Presenters for the Weekend of Prayer include Fr. Andrew Apostoli, CFR, host of EWTN Sunday Night Prime; and Fr.Brian Dunkle, S.J.
The weekend concludes with 10:00 AM Sunday Mass on March 13, 2016.
Attendees will spend the weekend Adoring and Loving Jesus Christ in the overall context of The New Evangelization for the World!!
Registration Form will be Available Soon
for 2016 Weekend of Prayer
Carol Weiler 11 Warbler New Orleans, LA 70124


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4 bedroom detached house for sale The Beeches Close, Sketty, SwanseaPA Black are pleased to offer for sale this substantial detached family home which is in immaculate condition throughout. Conveniently located in Sketty giving easy access to Singleton Hospital, Swansea University and the city centre. Four double bedrooms, dressing room and en-suite. Superb garde... More details ›
£549,999 Offers in Region of
Offers in Region of £549,999
Shop for sale Kittle Village Stores Pennard Road, Kittle, SA3 3JG Busy Post Office & Convenience Store Sought after rural village setting Excellent turnover and profits 4 bedroom family house More details ›
3 bedroom detached house for sale WEST CROSS LANE, West Cross, SA3This beautiful 1920s property is set in outstanding, private mature walled gardens with a fantastic array of exotic trees, shrubs and secluded seating area. Built in the late 1920s in the kitchen garden of the Duke of Beauforts summer residence, now a nursing home. More details ›
£535,000 Guide Price
Guide Price £535,000
5 bedroom detached house for sale Cadle Mill, Swansea, SA5Character cottage located in a delightful setting. About 2 acres. Sympathetically extended over the years. 3 reception rooms & conservatory. 5 bedrooms (1 en suite). Useful log cabin/studio. Further stone tool store & office area. (stms). With charming wood, gardens & stream. (contd...) More details ›
5 bedroom character property for sale Cadle Mill,Fforestfach,Swansea,SA5Castell Moel is a delightful stone built cottage thought to date mid c.1700s and has been sympathetically extended and renovated over theyears while retaining its charm and character. More details ›
4 bedroom detached house for sale Llanrhidian, Gower, SwanseaA traditional Gower Farmhouse with an abundance of charm and character, set in roughly eleven acres of grazing land, gardens and ancient woodland. West Penrhaullt Farm can be found at the end of a private driveway, set well back from the B4295 in the North Gower village of Llanrhidian. There are ... More details ›
2 bedroom apartment for sale Rotherslade Road, SA3A spacious ground floor two bedroom apartment located in an idyllic position occupying a very prominent position overlooking both Langland and Rotherslade Bays with un-interrupted views across the bay. More details ›
5 bedroom detached house for sale Slade Road, SA3A fine extended detached 1930s family home situated in a very quiet residential location at the bottom end of Slade road enjoying a lovely wooded aspect to the side and a private west facing rear garden. More details ›
4 bedroom detached house for sale The Nurseries, Oldway, Bishopston, SwanseaA brand new four bedroom detached house, forming part of the exclusive Redrow Homes, Nurseries development, in Bishopston. The 'Redmond' design captures the essence of traditional house building and offers generous family accommodation. Comprising; hall, with stairs to the first floor, storage cu... More details ›
£534,995 From
From £534,995
4 bedroom detached house for sale The Richmond at The Nurseries, Oldway, Bishopston, SA3Blending timeless Arts and Crafts touches with the finest of MODERN FAMILY LIVING, The Richmond is a home that is as beautiful as it is practical. This 4 bedroom home, set over 2030 square feet, offers a FANTASTIC QUALITY OF LIFE that exceeds the very HIGHEST STANDARDS. More details ›
Added on 16/01/2015 by Redrow Homes. Call: 029 2050 8121 Local call rate
Thank you.
Your information has been sent to 0 out of 69 agents and developers who have property to sell in the area you specified.


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HN-CLC109 Catskill
Guitar Cutting BoardItem # HN-CLC109
- Guitar shape is fun and practical
- Made of 100% responsibly harvested hardwood
- Reversible with juice gutter on 1 side
- Made in the USA
- Dimensions: 22x14.5x.75 inches
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Guitar Cutting Board
The beautiful hardwood Guitar Cutting Board easily wipes clean, but you won't be able to wipe the silly grin off your face while you use it. A perfect gift for the guitar fan and a must-have for your creative kitchen, this eye-catcher is practical too: made from 100% responsibly harvested hardwood by Catskill Craftsmen, it has a routed juice gutter on one side, or flip it over and use the smooth surface on the other. Added bonus: it's so much fun to look at, you won't have to put it away. About Cat


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With the Commonwealth Games just a few days away, the Government of Delhi and the Games Organizing Committee have designated Paan-stained walls, bus-stops and other similar sites in the city as "Community Art". The step was taken after the government realized that its original "civilizing mission" for the residents of the city was somewhere lost in the middle due to controversies over mismanagement and corruption in the games.


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Do people recognize their good or bad behavior before or after whatever they do? Or do they act without thinking?
SmartSweet1 51-55, F 3 Answers 2 Aug 14, 2012 in Parenting & Family
Some always just brush off the good behaviors in a person,and look for bad so that they can always try to bring down the person.
Best Answer
Depends. Some do, some don't. Some just react.
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Actually its a pretty honest, truthful and spot on answer. People are either aware, unaware, ignorant, or just don't care.
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i always realize good or bad afterward
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of course.
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Can't get enough "Game of Thrones"? Here's what to devour once you've finished every episode of HBO's show and the books it's based on.
The Very Large Telescope has spotted signs that may indicate the presence of the oldest stars in the universe -- formed from matter created by the Big Bang.
At E3 in Los Angeles, Hello Games developer Sean Murray gives a tour of the ambitious sandbox game that was introduced during last year's event.
In a letter to the attorneys general of New York and Connecticut, lawyers for the Universal Music Group say the label hasn't engaged in anticompetitive practices with Apple over free streams from Apple rivals like Spotify.
Microsoft unfolds a new accessory -- a platform-agnostic keyboard that works with the major mobile operating systems.
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Among the dozens of robots present at the New York trade show this week, one helps autistic children practice social skills and another is a roving kiosk for big-box stores.
Captain Kirk has met his most formidable opponent yet in this fan-made trailer for a fictional 1985 movie called "The Carbonite Maneuver." Kirk will find the Force is very strong with this villain.


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