Journal articles: 'Phages de type T4'

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Godon, Jean-Jacques, Ariane Bize, Hoang Ngo, Laurent Cauquil, Mathieu Almeida, Marie-Agnès Petit, and Olivier Zemb. "Bacterial Consumption of T4 Phages." Microorganisms 9, no. 9 (August 31, 2021): 1852. http://dx.doi.org/10.3390/microorganisms9091852.

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The bacterial consumption of viruses not been reported on as of yet even though bacteria feed on almost anything. Viruses are widely distributed but have no acknowledged active biocontrol. Viral biomass undoubtedly reintegrates trophic cycles; however, the mechanisms of this phase still remain unknown. 13C-labelled T4 phages monitor the increase of the density of the bacterial DNA concomitant with the decrease of plaque forming units. We used 12C T4 phages as a control. T4 phage disappearance in wastewater sludge was found to occur mainly through predation by Aeromonadacea. Phage consumption also favours significant in situ bacterial growth. Furthermore, an isolated strain of Aeromonas was observed to grow on T4 phages as sole the source of carbon, nitrogen, and phosphorus. Bacterial species are capable of consuming bacteriophages in situ, which is likely a widespread and underestimated type of biocontrol. This assay is anticipated as a starting point for harnessing the bacterial potential in limiting the diffusion of harmful viruses within environments such as in the gut or in water.

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Tétart, Françoise, Carine Desplats, Mzia Kutateladze, Caroline Monod, Hans-Wolfgang Ackermann, and H. M. Krisch. "Phylogeny of the Major Head and Tail Genes of the Wide-Ranging T4-Type Bacteriophages." Journal of Bacteriology 183, no. 1 (January 1, 2001): 358–66. http://dx.doi.org/10.1128/jb.183.1.358-366.2001.

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ABSTRACT We examined a number of bacteriophages with T4-type morphology that propagate in different genera of enterobacteria,Aeromonas, Burkholderia, andVibrio. Most of these phages had a prolate icosahedral head, a contractile tail, and a genome size that was similar to that of T4. A few of them had more elongated heads and larger genomes. All these phages are phylogenetically related, since they each had sequences homologous to the capsid gene (gene23), tail sheath gene (gene 18), and tail tube gene (gene 19) of T4. On the basis of the sequence comparison of their virion genes, the T4-type phages can be classified into three subgroups with increasing divergence from T4: the T-evens, pseudoT-evens, and schizoT-evens. In general, the phages that infect closely related host species have virion genes that are phylogenetically closer to each other than those of phages that infect distantly related hosts. However, some of the phages appear to be chimeras, indicating that, at least occasionally, some genetic shuffling has occurred between the different T4-type subgroups. The compilation of a number of gene 23 sequences reveals a pattern of conserved motifs separated by sequences that differ in the T4-type subgroups. Such variable patches in the gene 23sequences may determine the size of the virion head and consequently the viral genome length. This sequence analysis provides molecular evidence that phages related to T4 are widespread in the biosphere and diverged from a common ancestor in acquiring the ability to infect different host bacteria and to occupy new ecological niches.

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Chibani-Chennoufi, Sandra, Josette Sidoti, Anne Bruttin, Marie-Lise Dillmann, Elizabeth Kutter, Firdausi Qadri, Shafiqul Alam Sarker, and Harald Brüssow. "Isolation of Escherichia coli Bacteriophages from the Stool of Pediatric Diarrhea Patients in Bangladesh." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8287–94. http://dx.doi.org/10.1128/jb.186.24.8287-8294.2004.

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ABSTRACT A 3-week coliphage survey was conducted in stool samples from 140 Bangladeshi children hospitalized with severe diarrhea. On the Escherichia coli indicator strain K803, all but one phage isolate had 170-kb genomes and the morphology of T4 phage. In spot tests, the individual T4-like phages infected up to 27 out of 40 diarrhea-associated E. coli, representing 22 O serotypes and various virulence factors; only five of them were not infected by any of these new phages. A combination of diagnostic PCR based on g32 (DNA binding) and g23 (major capsid protein) and Southern hybridization revealed that half were T-even phages sensu strictu, while the other half were pseudo-T-even or even more distantly related T4-like phages that failed to cross-hybridize with T4 or between each other. Nineteen percent of the acute stool samples yielded T4-like phages, and the prevalence was lower in convalescent stool samples. T4-like phages were also isolated from environmental and sewage water, but with low frequency and low titers. On the enteropathogenic E. coli strain O127:K63, 14% of the patients yielded phage, all of which were members of the phage family Siphoviridae with 50-kb genomes, showing the morphology of Jersey- and beta-4 like phages and narrow lytic patterns on E. coli O serotypes. Three siphovirus types could be differentiated by lack of cross-hybridization. Only a few stool samples were positive on both indicator strains. Phages with closely related restriction patterns and, in the case of T4-like phages, identical g23 gene sequences were isolated from different patients, suggesting epidemiological links between the patients.

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Hammerl, J. A., C. Jackel, J. Reetz, S. Beck, T. Alter, R. Lurz, C. Barretto, H. Brussow, and S. Hertwig. "Campylobacter jejuni Group III Phage CP81 Contains Many T4-Like Genes without Belonging to the T4-Type Phage Group: Implications for the Evolution of T4 Phages." Journal of Virology 85, no. 17 (June 22, 2011): 8597–605. http://dx.doi.org/10.1128/jvi.00395-11.

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Letarov, A., X. Manival, C. Desplats, and H. M. Krisch. "gpwac of the T4-Type Bacteriophages: Structure, Function, and Evolution of a Segmented Coiled-Coil Protein That Controls Viral Infectivity." Journal of Bacteriology 187, no. 3 (February 1, 2005): 1055–66. http://dx.doi.org/10.1128/jb.187.3.1055-1066.2005.

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ABSTRACT The wac gene product (gpwac) or fibritin of bacteriophage T4 forms the six fibers that radiate from the phage neck. During phage morphogenesis these whiskers bind the long tail fibers (LTFs) and facilitate their attachment to the phage baseplate. After the cell lysis, the gpwac fibers function as part of an environmental sensing device that retains the LTFs in a retracted configuration and thus prevents phage adsorption in unfavorable conditions. A comparative analysis of the sequences of 5 wac gene orthologs from various T4-type phages reveals that the ∼50-amino-acid N-terminal domain is the only highly conserved segment of the protein. This sequence conservation is probably a direct consequence of the domain's strong and specific interactions with the neck proteins. The sequence of the central fibrous region of gpwac is highly plastic, with only the heptad periodicity of the coiled-coil structure being conserved. In the various gpwac sequences, the small C-terminal domain essential for initiation of the folding of T4 gpwac is replaced by unrelated sequences of unknown origin. When a distant T4-type phage has a novel C-terminal gpwac sequence, the phage's gp36 sequence that is located at the knee joint of the LTF invariably has a novel domain in its C terminus as well. The covariance of these two sequences is compatible with genetic data suggesting that the C termini of gpwac and gp36 engage in a protein-protein interaction that controls phage infectivity. These results add to the limited evidence for domain swapping in the evolution of phage structural proteins.

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Wang, Jiaying, Yan D. Niu, Jinding Chen, Hany Anany, Hans-W. Ackermann, Roger P. Johnson, Collins N. Ateba, Kim Stanford, and Tim A. McAllister. "Feces of feedlot cattle contain a diversity of bacteriophages that lyse non-O157 Shiga toxin-producing Escherichia coli." Canadian Journal of Microbiology 61, no. 7 (July 2015): 467–75. http://dx.doi.org/10.1139/cjm-2015-0163.

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This study aimed to isolate and characterize bacteriophages that lyse non-O157 Shiga toxin-producing Escherichia coli (STEC) from cattle feces. Of 37 non-O157 STEC-infecting phages isolated, those targeting O26 (AXO26A, AYO26A, AYO26B), O103 (AXO103A, AYO103A), O111 (AXO111A, AYO111A), O121 (AXO121A, AXO121B), and O145 (AYO145A, AYO145B) were further characterized. Transmission electron microscopy showed that the 11 isolates belonged to 3 families and 6 genera: the families Myoviridae (types rV5, T4, ViI, O1), Siphoviridae (type T5), and Podoviridae (type T7). Genome size of the phages as determined by pulsed-field gel electrophoresis ranged from 38 to 177 kb. Excluding phages AXO26A, AYO103A, AYO145A, and AYO145B, all other phages were capable of lysing more than 1 clinically important strain from serogroups of O26, O91, O103, O111, O113, O121, and O128, but none exhibited infectivity across all serogroups. Moreover, phages AYO26A, AXO121A, and AXO121B were also able to lyse 4 common phage types of STEC O157:H7. Our findings show that a diversity of non-O157 STEC-infecting phages are harbored in bovine feces. Phages AYO26A, AYO26B, AXO103A, AXO111A, AYO111A, AXO121A, and AXO121B exhibited a broad host range against a number of serogroups of STEC and have potential for the biocontrol of STEC in the environment.

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Büttner, Carina R., Yingzhou Wu, Karen L. Maxwell, and Alan R. Davidson. "Baseplate assembly of phage Mu: Defining the conserved core components of contractile-tailed phages and related bacterial systems." Proceedings of the National Academy of Sciences 113, no. 36 (August 23, 2016): 10174–79. http://dx.doi.org/10.1073/pnas.1607966113.

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Contractile phage tails are powerful cell puncturing nanomachines that have been co-opted by bacteria for self-defense against both bacteria and eukaryotic cells. The tail of phage T4 has long served as the paradigm for understanding contractile tail-like systems despite its greater complexity compared with other contractile-tailed phages. Here, we present a detailed investigation of the assembly of a “simple” contractile-tailed phage baseplate, that of Escherichia coli phage Mu. By coexpressing various combinations of putative Mu baseplate proteins, we defined the required components of this baseplate and delineated its assembly pathway. We show that the Mu baseplate is constructed through the independent assembly of wedges that are organized around a central hub complex. The Mu wedges are comprised of only three protein subunits rather than the seven found in the equivalent structure in T4. Through extensive bioinformatic analyses, we found that homologs of the essential components of the Mu baseplate can be identified in the majority of contractile-tailed phages and prophages. No T4-like prophages were identified. The conserved simple baseplate components were also found in contractile tail-derived bacterial apparatuses, such as type VI secretion systems, Photorhabdus virulence cassettes, and R-type tailocins. Our work highlights the evolutionary connections and similarities in the biochemical behavior of phage Mu wedge components and the TssF and TssG proteins of the type VI secretion system. In addition, we demonstrate the importance of the Mu baseplate as a model system for understanding bacterial phage tail-derived systems.

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Salem, Mabruka, Maria I. Pajunen, Jin Woo Jun, and Mikael Skurnik. "T4-like Bacteriophages Isolated from Pig Stools Infect Yersinia pseudotuberculosis and Yersinia pestis Using LPS and OmpF as Receptors." Viruses 13, no. 2 (February 13, 2021): 296. http://dx.doi.org/10.3390/v13020296.

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The Yersinia bacteriophages fPS-2, fPS-65, and fPS-90, isolated from pig stools, have long contractile tails and elongated heads, and they belong to genus Tequatroviruses in the order Caudovirales. The phages exhibited relatively wide host ranges among Yersinia pseudotuberculosis and related species. One-step growth curve experiments revealed that the phages have latent periods of 50–80 min with burst sizes of 44–65 virions per infected cell. The phage genomes consist of circularly permuted dsDNA of 169,060, 167,058, and 167,132 bp in size, respectively, with a G + C content 35.3%. The number of predicted genes range from 267 to 271. The phage genomes are 84–92% identical to each other and ca 85% identical to phage T4. The phage receptors were identified by whole genome sequencing of spontaneous phage-resistant mutants. The phage-resistant strains had mutations in the ompF, galU, hldD, or hldE genes. OmpF is a porin, and the other genes encode lipopolysaccharide (LPS) biosynthetic enzymes. The ompF, galU, and hldE mutants were successfully complemented in trans with respective wild-type genes. The host recognition was assigned to long tail fiber tip protein Gp38, analogous to that of T-even phages such as Salmonella phage S16, specifically to the distal β-helices connecting loops.

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Rabinovitch, Avinoam, Hilla Hadas, Monica Einav, Zeev Melamed, and Arieh Zaritsky. "Model for Bacteriophage T4 Development inEscherichia coli." Journal of Bacteriology 181, no. 5 (March 1, 1999): 1677–83. http://dx.doi.org/10.1128/jb.181.5.1677-1683.1999.

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ABSTRACT Mathematical relations for the number of mature T4 bacteriophages, both inside and after lysis of an Escherichia coli cell, as a function of time after infection by a single phage were obtained, with the following five parameters: delay time until the first T4 is completed inside the bacterium (eclipse period, ν) and its standard deviation (ς), the rate at which the number of ripe T4 increases inside the bacterium during the rise period (α), and the time when the bacterium bursts (μ) and its standard deviation (β). Burst size [B = α(μ − ν)], the number of phages released from an infected bacterium, is thus a dependent parameter. A least-squares program was used to derive the values of the parameters for a variety of experimental results obtained with wild-type T4 inE. coli B/r under different growth conditions and manipulations (H. Hadas, M. Einav, I. Fishov, and A. Zaritsky, Microbiology 143:179–185, 1997). A “destruction parameter” (ζ) was added to take care of the adverse effect of chloroform on phage survival. The overall agreement between the model and the experiment is quite good. The dependence of the derived parameters on growth conditions can be used to predict phage development under other experimental manipulations.

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ABEDON, STEPHEN T. "Bacteriophage T4 resistance to lysis-inhibition collapse." Genetical Research 74, no. 1 (August 1999): 1–11. http://dx.doi.org/10.1017/s0016672399003833.

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Lysis inhibition is a mechanism of latent-period extension and burst-size increase that is induced by the T4 bacteriophage adsorption of T4-infected cells. Mutants of T4 genes imm, sp and 5 (specifically the ts1 mutant of 5) display some lysis inhibition. However, these mutants experience lysis-inhibition collapse, the lysis of lysis-inhibited cells, earlier than wild-type-infected cells (i.e. their collapse occurs prematurely). Lysis from without is a lysis induced by excessive T4 adsorption. Gp5 is an inducer of lysis from without while gpimm and gpsp effect resistance to lysis from without. This paper shows that interfering with the adsorption of phages to imm-, sp- or 5ts1-mutant-infected cells, in a variety of contexts, inhibits premature lysis-inhibition collapse. From these data it is inferred that wild-type T4-infected cells display resistance to lysis-inhibition collapse by a mechanism resembling resistance to lysis from without.

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Gary, Todd P., Nancy E. Colowick, and Gisela Mosig. "A Species Barrier Between Bacteriophages T2 and T4: Exclusion, Join-Copy and Join-Cut-Copy Recombination and Mutagenesis in the dCTPase Genes." Genetics 148, no. 4 (April 1, 1998): 1461–73. http://dx.doi.org/10.1093/genetics/148.4.1461.

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Abstract Bacteriophage T2 alleles are excluded in crosses between T2 and T4 because of genetic isolation between these two virus species. The severity of exclusion varies in different genes, with gene 56, encoding an essential dCT(D)Pase/dUT(D)Pase of these phages, being most strongly affected. To investigate reasons for such strong exclusion, we have (1) sequenced the T2 gene 56 and an adjacent region, (2) compared the sequence with the corresponding T4 DNA, (3) constructed chimeric phages in which T2 and T4 sequences of this region are recombined, and (4) tested complementation, recombination, and exclusion with gene 56 cloned in a plasmid and in the chimeric phages in Escherichia coli CR63, in which growth of wild-type T2 is not restricted by T4. Our results argue against a role of the dCTPase protein in this exclusion and implicate instead DNA sequence differences as major contributors to the apparent species barrier. This sequence divergence exhibits a remarkable pattern: a major heterologous sequence counter-clockwise from gene 56 (and downstream of the gene 56 transcripts) replaces in T2 DNA the T4 gene 69. Gene 56 base sequences bordering this substituted region are significantly different, whereas sequences of the dam genes, adjacent in the clockwise direction, are similar in T2 and in T4. The gene 56 sequence differences can best be explained by multiple compensating frameshifts and base substitutions, which result in T2 and T4 dCTPases whose amino acid sequences and functions remain similar. Based on these findings we propose a model for the evolution of multiple sequence differences concomitant with the substitution of an adjacent gene by foreign DNA: invasion by the single-stranded segments of foreign DNA, nucleated from a short DNA sequence that was complementary by chance, has triggered recombination-dependent replication by “join-copy” and “join-cut-copy” pathways that are known to operate in the T-even phages and are implicated in other organisms as well. This invasion, accompanied by heteroduplex formation between partially similar sequences, and perhaps subsequent partial heteroduplex repair, simultaneously substituted T4 gene 69 for foreign sequences and scrambled the sequence of the dCTPase gene 56. We suggest that similar mechanisms can mobilize DNA segments for horizontal transfer without necessarily requiring transposase or site-specific recombination functions.

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Desplats, Carine, Christophe Dez, Françoise Tétart, Heïdy Eleaume, and H. M. Krisch. "Snapshot of the Genome of the Pseudo-T-Even Bacteriophage RB49." Journal of Bacteriology 184, no. 10 (May 15, 2002): 2789–804. http://dx.doi.org/10.1128/jb.184.10.2789-2804.2002.

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ABSTRACT RB49 is a virulent bacteriophage that infects Escherichia coli. Its virion morphology is indistinguishable from the well-known T-even phage T4, but DNA hybridization indicated that it was phylogenetically distant from T4 and thus it was classified as a pseudo-T-even phage. To further characterize RB49, we randomly sequenced small fragments corresponding to about 20% of the ≈170-kb genome. Most of these nucleotide sequences lacked sufficient homology to T4 to be detected in an NCBI BlastN analysis. However, when translated, about 70% of them encoded proteins with homology to T4 proteins. Among these sequences were the numerous components of the virion and the phage DNA replication apparatus. Mapping the RB49 genes revealed that many of them had the same relative order found in the T4 genome. The complete nucleotide sequence was determined for the two regions of RB49 genome that contain most of the genes involved in DNA replication. This sequencing revealed that RB49 has homologues of all the essential T4 replication genes, but, as expected, their sequences diverged considerably from their T4 homologues. Many of the nonessential T4 genes are absent from RB49 and have been replaced by unknown sequences. The intergenic sequences of RB49 are less conserved than the coding sequences, and in at least some cases, RB49 has evolved alternative regulatory strategies. For example, an analysis of transcription in RB49 revealed a simpler pattern of regulation than in T4, with only two, rather than three, classes of temporally controlled promoters. These results indicate that RB49 and T4 have diverged substantially from their last common ancestor. The different T4-type phages appear to contain a set of common genes that can be exploited differently, by means of plasticity in the regulatory sequences and the precise choice of a large group of facultative genes.

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Sanmukh, Swapnil Ganesh, Nilton José dos Santos, Caroline Nascimento Barquilha, Maira Smaniotto Cucielo, Márcio de Carvalho, Patricia Pintor dos Reis, Flávia Karina Delella, Hernandes F. Carvalho, and Sérgio Luis Felisbino. "Bacteriophages M13 and T4 Increase the Expression of Anchorage-Dependent Survival Pathway Genes and Down Regulate Androgen Receptor Expression in LNCaP Prostate Cell Line." Viruses 13, no. 9 (September 2, 2021): 1754. http://dx.doi.org/10.3390/v13091754.

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Wild-type or engineered bacteriophages have been reported as therapeutic agents in the treatment of several types of diseases, including cancer. They might be used either as naked phages or as carriers of antitumor molecules. Here, we evaluate the role of bacteriophages M13 and T4 in modulating the expression of genes related to cell adhesion, growth, and survival in the androgen-responsive LNCaP prostatic adenocarcinoma-derived epithelial cell line. LNCaP cells were exposed to either bacteriophage M13 or T4 at a concentration of 1 × 105 pfu/mL, 1 × 106 pfu/mL, and 1 × 107 pfu/mL for 24, 48, and 72 h. After exposure, cells were processed for general morphology, cell viability assay, and gene expression analyses. Neither M13 nor T4 exposure altered cellular morphology, but both decreased the MTT reduction capacity of LNCaP cells at different times of treatment. In addition, genes AKT, ITGA5, ITGB1, ITGB3, ITGB5, MAPK3, and PI3K were significantly up-regulated, whilst the genes AR, HSPB1, ITGAV, and PGC1A were down-regulated. Our results show that bacteriophage M13 and T4 interact with LNCaP cells and effectively promote gene expression changes related to anchorage-dependent survival and androgen signaling. In conclusion, phage therapy may increase the response of PCa treatment with PI3K/AKT pathway inhibitors.

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Petrov, Vasiliy M., Swarnamala Ratnayaka, and Jim D. Karam. "Genetic Insertions and Diversification of the PolB-Type DNA Polymerase (gp43) of T4-Related Phages." Journal of Molecular Biology 395, no. 3 (January 2010): 457–74. http://dx.doi.org/10.1016/j.jmb.2009.10.054.

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Miller, Eric S., John F. Heidelberg, Jonathan A. Eisen, William C. Nelson, A. Scott Durkin, Ann Ciecko, Tamara V. Feldblyum, et al. "Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage." Journal of Bacteriology 185, no. 17 (September 1, 2003): 5220–33. http://dx.doi.org/10.1128/jb.185.17.5220-5233.2003.

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ABSTRACT The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.

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Wang, Fei Jun, and Lynn S. Ripley. "The Spectrum of Acridine Resistant Mutants of Bacteriophage T4 Reveals Cryptic Effects of the tsL141 DNA Polymerase Allele on Spontaneous Mutagenesis." Genetics 148, no. 4 (April 1, 1998): 1655–65. http://dx.doi.org/10.1093/genetics/148.4.1655.

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Abstract Mutations in the ac gene of bacteriophage T4 confer resistance to acridine-inhibition of phage development. Previous studies had localized the ac gene region; we show that inactivation of T4 Open Reading Frame 52.2 confers the Acr phenotype. Thus, 52.2 is ac. The resistance mechanism is unknown. The ac gene provides a convenient forward mutagenesis assay. Its compact size (156 bp) simplifies mutant sequencing and diverse mutant types are found: base substitutions leading to missense or nonsense codons, inframe deletions or duplications within the coding sequence, deletion or duplication frameshifts, insertions, complex mutations, and large deletions extending into neighboring sequences. Comparisons of spontaneous mutagenesis between phages bearing the wild-type or tsL141 alleles of DNA polymerase demonstrate that the impact of the mutant polymerase is cryptic when total spontaneous mutant frequencies are compared, but the DNA sequences of the ac mutants reveal a substantial alteration of fidelity by the mutant polymerase. The patterns of base substitution mutagenesis suggest that some site-specific mutation rate effects may reflect hotspots for mutagenesis arising by different mechanisms. A new class of spontaneous duplication mutations, having sequences inconsistent with misaligned pairing models, but consistent with nick-processing errors, has been identified at a hotspot in ac.

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Shuji, Kanamaru, Uchida Kazuya, Momiyama Takahiro, Nishijo Kaname, and Arisaka Fumio. "1P016 Structure and function of receptor binding proteins of T4-type phages and T2-type phages(Protein: Structure,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))." Seibutsu Butsuri 54, supplement1-2 (2014): S143. http://dx.doi.org/10.2142/biophys.54.s143_4.

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Shneider, Mikhail, Sergey Buth, Brian Ho, Marek Basler, John Mekalanos, and Petr Leiman. "Central spike proteins of contractile ejection systems." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C579. http://dx.doi.org/10.1107/s2053273314094200.

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Contractile tails of bacteriophages and related systems - R-type pyocins, the Serratia entomophila antifeeding prophage, the Photorhabdus Virulence Cassette, and the Type VI Secretion System (T6SS) - contain a special spike-shaped protein complex, which is involved in breaching the target cell envelope during infection. We have identified the genes and determined crystal structures for several spike proteins from phages, pyocins, and T6SS, and established a paradigm for their organization and function. The architecture of spike proteins is remarkably well conserved at the level of tertiary structure, but the corresponding genes and amino acid sequences have undergone huge rearrangements with domains becoming separate genes that are very far away from each other in the genome. Large bacteriophages and T6SS have the most complex spikes, in which the tip is a small protein that forms a very sharp conical extension on the spike. The membrane-attacking tip is stabilized by a buried Fe or Zn ion. The spike tip proteins belong to the PAAR (Proline-Alanine-Alanine-aRginine) repeat domain superfamily with several thousand members in the GenBank. PAAR repeat proteins from T6SS are often extended by a domain with a putative effector function (nuclease, DNases, peptidases, etc.) or by a transthyretin domain. PAAR knockout mutants of Vibrio cholerae and Acinetobacter baylyi have either reduced or completely abolished T6SS activity, showing that PAAR proteins are essential for T6SS function and can play an important role in building of the T6SS machine and/or target cell membrane piercing. The unique HMM profile of PAAR repeat proteins makes it possible to identify their orthologs in all T6SS and contractile tail phages including T4, phiKZ, P1, etc. Complete structures (including the tip protein) of phage T4 central spike and T6SS spike of Vibrio cholerae will be presented and discussed.

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Pineda, Melissa, Brian D. Gregory, Bridget Szczypinski, Kimberly R. Baxter, Ann Hochschild, Eric S. Miller, and Deborah M. Hinton. "A Family of Anti-σ70 Proteins in T4-type Phages and Bacteria that are Similar to AsiA, a Transcription Inhibitor and Co-activator of Bacteriophage T4." Journal of Molecular Biology 344, no. 5 (December 2004): 1183–97. http://dx.doi.org/10.1016/j.jmb.2004.10.003.

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Liu, Junjie, Zhenhua Yu, Xinzhen Wang, Jian Jin, Xiaobing Liu, and Guanghua Wang. "The distribution characteristics of the major capsid gene (g23) of T4-type phages in paddy floodwater in Northeast China." Soil Science and Plant Nutrition 62, no. 2 (March 3, 2016): 133–39. http://dx.doi.org/10.1080/00380768.2016.1163507.

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Boltovets, P., R. Radutny, V. Petlyovana, and T. Shevchenko. "INTERACTION BETWEEN PHAGES AND BACTERIA AS A TOOL FOR THE OBTAINING OF IMAGES." Bulletin of Taras Shevchenko National University of Kyiv. Series: Biology 72, no. 2 (2016): 69–71. http://dx.doi.org/10.17721/1728_2748.2016.72.69-71.

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The obtaining of images by lytic action of bacteriophage T4 on the Escherichia coli bacterial lawn is considered. Methodical aspects of the approach are discussed, namely, use of different stencil types, total and partial staining of obtained image by different dyes. The perspectives of the practical use are proposed namely restriction of the action of microorganisms in out-of-theway places etc.

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Arbiol, Christine, André M. Comeau, Mzia Kutateladze, Revaz Adamia, and H. M. Krisch. "Mobile Regulatory Cassettes Mediate Modular Shuffling in T4-Type Phage Genomes." Genome Biology and Evolution 2 (January 1, 2010): 140–52. http://dx.doi.org/10.1093/gbe/evq006.

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Chen, Chiy-Rong, Ching-Hsuan Lin, Juey-Wen Lin, Chi-I. Chang, Yi-Hsiung Tseng, and Shu-Fen Weng. "Characterization of a novel T4-type Stenotrophomonas maltophilia virulent phage Smp14." Archives of Microbiology 188, no. 2 (April 18, 2007): 191–97. http://dx.doi.org/10.1007/s00203-007-0238-5.

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Cao, Yong-Chang, Quan-Cheng Shi, Jing-Yun Ma, Qing-Mei Xie, and Ying-Zuo Bi. "Vaccination against Very Virulent Infectious Bursal Disease Virus Using Recombinant T4 Bacteriophage Displaying Viral Protein VP2." Acta Biochimica et Biophysica Sinica 37, no. 10 (October 1, 2005): 657–64. http://dx.doi.org/10.1111/j.1745-7270.2005.00101.x.

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AbstractIn order to develop a desirable inexpensive, effective and safe vaccine against the very virulent infectious bursal disease virus (vvIBDV), we tried to take advantage of the emerging T4 bacteriophage surface protein display system. The major immunogen protein VP2 from the vvIBDV strain HK46 was fused to the nonessential T4 phage surface capsid protein, a small outer capsid (SOC) protein, resulting in the 49 kDa SOC-VP2 fusion protein, which was verified by sodium dodecylsulfate polyacrylamide gel electrophoresis and Western blot. Immunoelectromicroscopy showed that the recombinant VP2 protein was successfully displayed on the surface of the T4 phage. The recombinant VP2 protein is antigenic and showed reactivities to various monoclonal antibodies (mAbs) against IBDV, whereas the wild-type phage T4 could not react to any mAb. In addition, the recombinant VP2 protein is immunogenic and elicited specific antibodies in immunized specific pathogen free (SPF) chickens. More significantly, immunization of SPF chickens with the recombinant T4-VP2 phage protected them from infection by the vvIBDV strain HK46. When challenged with the vvIBDV strain HK46 at a dose of 100 of 50% lethal dose (LD50) per chicken 4 weeks after the booster was given, the group vaccinated with the T4-VP2 recombinant phage showed no clinical signs of disease or death, whereas the unvaccinated group and the group vaccinated with the wild-type T4 phage exhibited 100% clinical signs of disease and bursal damages, and 30%-40% mortality. Collectively, the data herein showed that the T4-displayed VP2 protein might be an inexpensive, effective and safe vaccine candidate against vvIBDV.

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Tiemann, Bernd, Reinhard Depping, Egle Gineikiene, Laura Kaliniene, Rimas Nivinskas, and Wolfgang Rüger. "ModA and ModB, Two ADP-Ribosyltransferases Encoded by Bacteriophage T4: Catalytic Properties and Mutation Analysis." Journal of Bacteriology 186, no. 21 (November 1, 2004): 7262–72. http://dx.doi.org/10.1128/jb.186.21.7262-7272.2004.

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ABSTRACT Bacteriophage T4 encodes three ADP-ribosyltransferases, Alt, ModA, and ModB. These enzymes participate in the regulation of the T4 replication cycle by ADP-ribosylating a defined set of host proteins. In order to obtain a better understanding of the phage-host interactions and their consequences for regulating the T4 replication cycle, we studied cloning, overexpression, and characterization of purified ModA and ModB enzymes. Site-directed mutagenesis confirmed that amino acids, as deduced from secondary structure alignments, are indeed decisive for the activity of the enzymes, implying that the transfer reaction follows the Sn1-type reaction scheme proposed for this class of enzymes. In vitro transcription assays performed with Alt- and ModA-modified RNA polymerases demonstrated that the Alt-ribosylated polymerase enhances transcription from T4 early promoters on a T4 DNA template, whereas the transcriptional activity of ModA-modified polymerase, without the participation of T4-encoded auxiliary proteins for middle mode or late transcription, is reduced. The results presented here support the conclusion that ADP-ribosylation of RNA polymerase and of other host proteins allows initial phage-directed mRNA synthesis reactions to escape from host control. In contrast, subsequent modification of the other cellular target proteins limits transcription from phage early genes and participates in redirecting transcription to phage middle and late genes.

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Clokie, Martha R. J., Jinyu Shan, Shaun Bailey, Ying Jia, Henry M. Krisch, Stephen West, and Nicholas H. Mann. "Transcription of a 'photosynthetic' T4-type phage during infection of a marine cyanobacterium." Environmental Microbiology 8, no. 5 (May 2006): 827–35. http://dx.doi.org/10.1111/j.1462-2920.2005.00969.x.

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Golec, Piotr, Joanna Karczewska-Golec, Birgit Voigt, Dirk Albrecht, Thomas Schweder, Michael Hecker, Grzegorz Węgrzyn, and Marcin Łoś. "Proteomic profiles and kinetics of development of bacteriophage T4 and its rI and rIII mutants in slowly growing Escherichia coli." Journal of General Virology 94, no. 4 (April 1, 2013): 896–905. http://dx.doi.org/10.1099/vir.0.048686-0.

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Bacteriophage T4 survival in its natural environment requires adjustment of phage development to the slow bacterial growth rate or the initiation of mechanisms of pseudolysogeny or lysis inhibition (LIN). While phage-encoded RI and probably RIII proteins seem to be crucial players in pseudolysogeny and LIN phenomena, the identity of proteins involved in the regulation of T4 development in slowly growing bacteria has remained unknown. In this work, using a chemostat system, we studied the development of wild-type T4 (T4wt) and its rI (T4rI) and rIII (T4rIII) mutants in slowly growing bacteria, where T4 did not initiate LIN or pseudolysogeny. We determined eclipse periods, phage propagation times, latent periods and burst sizes of T4wt, T4rI and T4rIII. We also compared intracellular proteomes of slowly growing Escherichia coli infected with either T4wt or the mutants. Using two-dimensional PAGE analyses we found 18 differentially expressed proteins from lysates of infected cells. Proteins whose amounts were different in cells harbouring T4wt and the mutants are involved in processes of replication, phage–host interactions or they constitute virion components. Our data indicate that functional RI and RIII proteins – apart from their already known roles in LIN and pseudolysogeny – are also necessary for the regulation of phage T4 development in slowly growing bacteria. This regulation may be more complicated than previously anticipated, with many factors influencing T4 development in its natural habitat.

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Barry, Jack, Mei Lie Wong,, and Bruce Alberts. "In vitro reconstitution of DNA replication initiated by genetic recombination: a T4 bacteriophage model for a type of DNA synthesis important for all cells." Molecular Biology of the Cell 30, no. 1 (January 2019): 146–59. http://dx.doi.org/10.1091/mbc.e18-06-0386.

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Using a mixture of 10 purified DNA replication and DNA recombination proteins encoded by the bacteriophage T4 genome, plus two homologous DNA molecules, we have reconstituted the genetic recombination–initiated pathway that initiates DNA replication forks at late times of T4 bacteriophage infection. Inside the cell, this recombination-dependent replication (RDR) is needed to produce the long concatemeric T4 DNA molecules that serve as substrates for packaging the shorter, genome-sized viral DNA into phage heads. The five T4 proteins that catalyze DNA synthesis on the leading strand, plus the proteins required for lagging-strand DNA synthesis, are essential for the reaction, as are a special mediator protein (gp59) and a Rad51/RecA analogue (the T4 UvsX strand-exchange protein). Related forms of RDR are widespread in living organisms—for example, they play critical roles in the homologous recombination events that can restore broken ends of the DNA double helix, restart broken DNA replication forks, and cross over chromatids during meiosis in eukaryotes. Those processes are considerably more complex, and the results presented here should be informative for dissecting their detailed mechanisms.

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29

Wu, Lii-Tzu, Shu-Ying Chang, Ming-Ren Yen, Tsuey-Ching Yang, and Yi-Hsiung Tseng. "Characterization of Extended-Host-Range Pseudo-T-Even Bacteriophage Kpp95 Isolated on Klebsiella pneumoniae." Applied and Environmental Microbiology 73, no. 8 (March 2, 2007): 2532–40. http://dx.doi.org/10.1128/aem.02113-06.

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ABSTRACT Kpp95, isolated on Klebsiella pneumoniae, is a bacteriophage with the morphology of T4-type phages and is capable of rapid lysis of host cells. Its double-stranded genomic DNA (ca. 175 kb, estimated by pulsed-field gel electrophoresis) can be cut only by restriction endonucleases with a cleavage site flanked either by A and T or by T, as tested, suggesting that it contains the modified derivative(s) of G and/or C. Over 26 protein bands were visualized upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the virion proteins. N-terminal sequencing indicated that the most abundant band (46 kDa) is the major coat protein (gp23) which has been cleaved from a signal peptide likely with a length similar to that of T4. Phylogenetic analyses based on the sequences of the central region (263 amino acid residues) of gp23 and the full length of gp18 and gp19 placed Kpp95 among the pseudo-T-even subgroup, most closely related to the coliphage JS98. In addition to being able to lyse many extended-spectrum β-lactamase strains of K. pneumoniae, Kpp95 can lyse Klebsiella oxytoca, Enterobacter agglomerans, and Serratia marcescens cells. Thus, Kpp95 deserves further studies for development as a component of a therapeutic cocktail, owing to its high efficiencies of host lysis plus extended host range.

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Matsumura, M., W. J. Becktel, M. Levitt, and B. W. Matthews. "Stabilization of phage T4 lysozyme by engineered disulfide bonds." Proceedings of the National Academy of Sciences 86, no. 17 (September 1989): 6562–66. http://dx.doi.org/10.1073/pnas.86.17.6562.

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Four different disulfide bridges (linking positions 9-164, 21-142, 90-122, and 127-154) were introduced into a cysteine-free phage T4 lysozyme at sites suggested by theoretical calculations and computer modeling. The new cysteines spontaneously formed disulfide bonds on exposure to air in vitro. In all cases the oxidized (crosslinked) lysozyme was more stable than the corresponding reduced (noncrosslinked) enzyme toward thermal denaturation. Relative to wild-type lysozyme, the melting temperatures of the 9-164 and 21-142 disulfide mutants were increased by 6.4 degrees C and 11.0 degrees C, whereas the other two mutants were either less stable or equally stable. Measurement of the equilibrium constants for the reduction of the engineered disulfide bonds by dithiothreitol indicates that the less thermostable mutants tend to have a less favorable crosslink in the native structure. The two disulfide bridges that are most effective in increasing the stability of T4 lysozyme have, in common, a large loop size and a location that includes a flexible part of the molecule. The results suggest that stabilization due to the effect of the crosslink on the entropy of the unfolded polypeptide is offset by the strain energy associated with formation of the disulfide bond in the folded protein. The design of disulfide bridges is discussed in terms of protein flexibility.

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31

Yoong, Sze Lin, Jacklyn Jackson, Courtney Barnes, Nicole Pearson, Taren Swindle, Sharleen O’Reilly, Rachel Tabak, Regina Belski, Alison Brown, and Rachel Sutherland. "Changing landscape of nutrition and dietetics research? A bibliographic analysis of top-tier published research in 1998 and 2018." Public Health Nutrition 24, no. 6 (January 13, 2021): 1318–27. http://dx.doi.org/10.1017/s1368980021000136.

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AbstractObjective:The current study sought to describe and compare study type, research design and translation phase of published research in nutrition and dietetic journals in 1998 and 2018.Design:This was a repeat cross-sectional bibliographic analysis of Nutrition and Dietetics research. All eligible studies in the top eight Nutrition and Dietetics indexed journals in 1998 and 2018 were included. Two independent reviewers coded each study for research design (study type and study design) and translation phase (T0-T4) of the research using seminal texts in the field.Setting:Not relevant.Participants:Not relevant.Results:The number of publications (1998, n 1030; 2018, n 1016) has not changed over time, but the research type, design and translation phases have. The proportion of intervention studies in 1998 (43·8 %) was significantly higher than 2018 (19·4 %). In 2018, more reviews (46·9 % v. 15·6 % in 1998) and less randomised trials (14·3 % v. 37·8 % in 1998) were published. In regard to translation phase, there was a higher proportion of T2–T4 research in 2018 (18·3 % v. 3·8 % in 1998); however, the proportion of T3/T4 (dissemination, implementation and population-level research) research was still low (<3 %). Our sensitivity analysis with the four journals that remained in the top eight journal across the two time periods found no differences in the research type, design and translation phases across time.Conclusions:There was a reduction in intervention and T0 publications, alongside higher publication of clinical study designs over time; however, published T3/T4 research in Nutrition and Dietetics is low. A greater focus on publishing interventions and dissemination and implementation may be needed.

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Qu, Yun, Paul Hyman, Timothy Harrah, and Edward Goldberg. "In Vivo Bypass of Chaperone by Extended Coiled-Coil Motif in T4 Tail Fiber." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8363–69. http://dx.doi.org/10.1128/jb.186.24.8363-8369.2004.

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ABSTRACT The distal-half tail fiber of bacteriophage T4 is made of three gene products: trimeric gp36 and gp37 and monomeric gp35. Chaperone P38 is normally required for folding gp37 peptides into a P37 trimer; however, a temperature-sensitive mutation in T4 (ts3813) that suppresses this requirement at 30°C but not at 42°C was found in gene 37 (R. J. Bishop and W. B. Wood, Virology 72:244-254, 1976). Sequencing of the temperature-sensitive mutant revealed a 21-bp duplication of wild-type gene 37 inserted into its C-terminal portion (S. Hashemolhosseini et al., J. Mol. Biol. 241:524-533, 1994). We noticed that the 21-amino-acid segment encompassing this duplication in the ts3813 mutant has a sequence typical of a coiled coil and hypothesized that its extension would relieve the temperature sensitivity of the ts3813 mutation. To test our hypothesis, we crossed the T4 ts3813 mutant with a plasmid encoding an engineered pentaheptad coiled coil. Each of the six mutants that we examined retained two amber mutations in gene 38 and had a different coiled-coil sequence varying from three to five heptads. While the sequences varied, all maintained the heptad-repeating coiled-coil motif and produced plaques at up to 50°C. This finding strongly suggests that the coiled-coil motif is a critical factor in the folding of gp37. The presence of a terminal coiled-coil-like sequence in the tail fiber genes of 17 additional T-even phages implies the conservation of this mechanism. The increased melting temperature should be useful for “clamps” to initiate the folding of trimeric β-helices in vitro and as an in vivo screen to identify, sequence, and characterize trimeric coiled coils.

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Liang, Y. M., R. X. Wei, T. Hsu, C. Alford, M. Dawson, and J. Karam. "Autogenous regulation of the regA gene of bacteriophage T4: derepression of translation." Genetics 119, no. 4 (August 1, 1988): 743–49. http://dx.doi.org/10.1093/genetics/119.4.743.

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Abstract The regA gene of phage T4 encodes a translational repressor that inhibits utilization of its own mRNA as well as the translation of a number of other phage-induced mRNAs. In recombinant plasmids, autogenous translational repression limits production of the RegA protein when the cloned structural gene is expressed under control of a strong, plasmid-borne promoter (lambda PL). We have found that a genetic fusion which places the regA ribosome binding domain in proximity to active translation leads to partial derepression of wild-type RegA protein synthesis. The derepression is not due to increased synthesis of regA RNA, suggesting that it occurs at the translational level. Derepressed clones of the wild-type regA gene were used to overproduce and purify the repressor. In an in vitro assay the wild-type target was sensitive and a mutant target was resistant to inhibition by the added protein. The results suggest that the sensitivity of a regA-regulated cistron to translational repression may depend on the competition between ribosomes and RegA protein for overlapping recognition sequences in the translation initiation domain of the mRNA.

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Mann, Nicholas H., Martha R. J. Clokie, Andrew Millard, Annabel Cook, William H. Wilson, Peter J. Wheatley, Andrey Letarov, and H. M. Krisch. "The Genome of S-PM2, a “Photosynthetic” T4-Type Bacteriophage That Infects Marine Synechococcus Strains." Journal of Bacteriology 187, no. 9 (May 1, 2005): 3188–200. http://dx.doi.org/10.1128/jb.187.9.3188-3200.2005.

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ABSTRACT Bacteriophage S-PM2 infects several strains of the abundant and ecologically important marine cyanobacterium Synechococcus. A large lytic phage with an isometric icosahedral head, S-PM2 has a contractile tail and by this criterion is classified as a myovirus (1). The linear, circularly permuted, 196,280-bp double-stranded DNA genome of S-PM2 contains 37.8% G+C residues. It encodes 239 open reading frames (ORFs) and 25 tRNAs. Of these ORFs, 19 appear to encode proteins associated with the cell envelope, including a putative S-layer-associated protein. Twenty additional S-PM2 ORFs have homologues in the genomes of their cyanobacterial hosts. There is a group I self-splicing intron within the gene encoding the D1 protein. A total of 40 ORFs, organized into discrete clusters, encode homologues of T4 proteins involved in virion morphogenesis, nucleotide metabolism, gene regulation, and DNA replication and repair. The S-PM2 genome encodes a few surprisingly large (e.g., 3,779 amino acids) ORFs of unknown function. Our analysis of the S-PM2 genome suggests that many of the unknown S-PM2 functions may be involved in the adaptation of the metabolism of the host cell to the requirements of phage infection. This hypothesis originates from the identification of multiple phage-mediated modifications of the host's photosynthetic apparatus that appear to be essential for maintaining energy production during the lytic cycle.

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James, Tamara D., Michael Cashel, and Deborah M. Hinton. "A Mutation within the β Subunit of Escherichia coli RNA Polymerase Impairs Transcription from Bacteriophage T4 Middle Promoters." Journal of Bacteriology 192, no. 21 (August 20, 2010): 5580–87. http://dx.doi.org/10.1128/jb.00338-10.

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ABSTRACT During infection of Escherichia coli, bacteriophage T4 usurps the host transcriptional machinery, redirecting it to the expression of early, middle, and late phage genes. Middle genes, whose expression begins about 1 min postinfection, are transcribed both from the extension of early RNA into middle genes and by the activation of T4 middle promoters. Middle-promoter activation requires the T4 transcriptional activator MotA and coactivator AsiA, which are known to interact with σ70, the specificity subunit of RNA polymerase. T4 motA amber [motA(Am)] or asiA(Am) phage grows poorly in wild-type E. coli. However, previous work has found that T4 motA(Am)does not grow in the E. coli mutant strain TabG. We show here that the RNA polymerase in TabG contains two mutations within its β-subunit gene: rpoB(E835K) and rpoB(G1249D). We find that the G1249D mutation is responsible for restricting the growth of either T4 motA(Am)or asiA(Am) and for impairing transcription from MotA/AsiA-activated middle promoters in vivo. With one exception, transcription from tested T4 early promoters is either unaffected or, in some cases, even increases, and there is no significant growth phenotype for the rpoB(E835K G1249D) strain in the absence of T4 infection. In reported structures of thermophilic RNA polymerase, the G1249 residue is located immediately adjacent to a hydrophobic pocket, called the switch 3 loop. This loop is thought to aid in the separation of the RNA from the DNA-RNA hybrid as RNA enters the RNA exit channel. Our results suggest that the presence of MotA and AsiA may impair the function of this loop or that this portion of the β subunit may influence interactions among MotA, AsiA, and RNA polymerase.

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Lossi, Nadine S., Rana Dajani, Paul Freemont, and Alain Filloux. "Structure–function analysis of HsiF, a gp25-like component of the type VI secretion system, in Pseudomonas aeruginosa." Microbiology 157, no. 12 (December 1, 2011): 3292–305. http://dx.doi.org/10.1099/mic.0.051987-0.

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Bacterial pathogens use a range of protein secretion systems to colonize their host. One recent addition to this arsenal is the type VI secretion system (T6SS), which is found in many Gram-negative bacteria. The T6SS involves 12–15 components, including a ClpV-like AAA+ ATPase. Moreover, the VgrG and Hcp components have been proposed to form a puncturing device, based on structural similarity to the tail spike components gp5/gp27 and the tail tube component gp19 of the T4 bacteriophage, respectively. Another T6SS component shows similarity to a T4 phage protein, namely gp25. The gp25 protein has been proposed to have lysozyme activity. Other T6SS components do not exhibit obvious similarity to characterized T4 phage components. The genome of Pseudomonas aeruginosa contains three T6SS gene clusters. In each cluster a gene encoding a putative member of the gp25-like protein family was identified, which we called HsiF. We confirmed this similarity by analysing the structure of the P. aeruginosa HsiF proteins using secondary and tertiary structure prediction tools. We demonstrated that HsiF1 is crucial for the T6SS-dependent secretion of Hcp and VgrG. Importantly, lysozyme activity of HsiF proteins was not detectable, and we related this observation to the demonstration that HsiF1 localizes to the cytoplasm of P. aeruginosa. Finally, our data showed that a conserved glutamate, predicted to be required for proper HsiF folding, is essential for its function. In conclusion, our data confirm the central role of HsiF in the T6SS mechanism, provide information on the predicted HsiF structure, and call for reconsideration of the function of gp25-like proteins.

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Karst, M., R. Dutkiewicz, T. Hahn, and K. Botzenhart. "The Difficulty of Using Coliphages as “Indicators” and “Index” Organisms." Water Science and Technology 24, no. 2 (July 1, 1991): 245–50. http://dx.doi.org/10.2166/wst.1991.0067.

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Different types of coliphages (T2, T4, T7, MS2 ϕX174, coliphages from surface water) were concentrated by a MgCl2 flocculation and a filtration (Virosorb 1MDS) method. Phage type as well as water quality had an influence on recovery rates of the concentration methods. None of them were superior when single phage types were used. Also various conditions had an influence on recovery rates in the direct plaque assay. Different phage aggregates are probably responsible for the range of recovery rates. Therefore it is probably not possible to standardize methods for isolating and detecting coliphages and they may be used as “indicators” or “index” organisms not at all or only in a strictly defined system.

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Carlson, Karin, and Aud Ȗvervatin. "BACTERIOPHAGE T4 ENDONUCLEASES II AND IV, OPPOSITELY AFFECTED BY dCMP HYDROXYMETHYLASE ACTIVITY, HAVE DIFFERENT ROLES IN THE DEGRADATION AND IN THE RNA POLYMERASE-DEPENDENT REPLICATION OF T4 CYTOSINE-CONTAINING DNA." Genetics 114, no. 3 (November 1, 1986): 669–85. http://dx.doi.org/10.1093/genetics/114.3.669.

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ABSTRACT Bacteriophage T4 mutants defective in gene 56 (dCTPase) synthesize DNA where cytosine (Cyt) partially or completely replaces hydroxymethylcytosine (HmCyt). This Cyt-DNA is degraded in vivo by T4 endonucleases II and IV, and by the exonuclease coded or controlled by genes 46 and 47.—Our results demonstrate that T4 endonuclease II is the principal enzyme initiating degradation of T4 Cyt-DNA. The activity of endonuclease IV, but not that of endonuclease II, was stimulated in the presence of a wild-type dCMP hydroxymethylase, also when no HmCyt was incorporated into phage DNA, suggesting the possibility of direct endonuclease IV-dCMP hydroxymethylase interactions. Endonuclease II activity, on the other hand, was almost completely inhibited in the presence of very small amounts of HmCyt (3-9% of total Cyt + HmCyt) in the DNA. Possible mechanisms for this inhibition are discussed.—The E. coli RNA polymerase modified by the products of T4 genes 33 and 55 was capable of initiating DNA synthesis on a Cyt-DNA template, although it probably cannot do so on an HmCyt template. In the presence of an active endonuclease IV, Cyt-DNA synthesis was arrested 10-30 min after infection, probably due to damage to the template. Cyt-DNA synthesis dependent on the unmodified (33 - 55 -) RNA polymerase was less sensitive to endonuclease IV action.

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Linder, Claës H., and Karin Carlson. "ESCHERICHIA COLI RHO FACTOR IS INVOLVED IN LYSIS OF BACTERIOPHAGE T4-INFECTED CELLS." Genetics 111, no. 2 (October 1, 1985): 197–218. http://dx.doi.org/10.1093/genetics/111.2.197.

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ABSTRACT A Rid (Rho interaction deficient) phenotype of bacteriophage T4 mutants was defined by cold-sensitive restriction (lack of plaque formation) on rho + hosts carrying additional polar mutations in unrelated genes, coupled to suppression (plaque formation) in otherwise isogenic strains carrying either a polarity-suppressing rho or a multicopy plasmid expressing the rho + allele. This suggests that the restriction may be due to lower levels of Rho than what is available to T4 in the suppressing strains.—Rid394×4 was isolated upon hydroxylamine mutagenesis and mapped in the t gene; other t mutants (and mot, as well as dda dexA double mutants) also showed a Rid phenotype. In liquid culture in strains that restricted plaque formation Rid394×4 showed strong lysis inhibition (a known t - phenotype) but no prolonged phage production (another well-known t - phenotype). This implies that when Rho is limiting the t mutant shuts off phage production at the normal time. Lysis inhibition was partially relieved, and phage production prolonged to varying extents depending on growth conditions in strains that allowed plaque formation. No significant effects on early gene expression were found. Apparently, both mutant (polarity-suppressing) and wild-type Rho can function in prolonging phage production and partially relieving lysis inhibition of Rid394×4 when present at a sufficiently high level, and Rho may play other role(s) in T4 development than in early gene regulation.

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Singla, Brijesh, Viwat Krisdhasima, and Joseph McGuire. "Adsorption Kinetics of Wild Type and Two Synthetic Stability Mutants of T4 Phage Lysozyme at Silanized Silica Surfaces." Journal of Colloid and Interface Science 182, no. 1 (September 1996): 292–96. http://dx.doi.org/10.1006/jcis.1996.0463.

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Dudas, Kathleen C., and Kenneth N. Kreuzer. "UvsW Protein Regulates Bacteriophage T4 Origin-Dependent Replication by Unwinding R-Loops." Molecular and Cellular Biology 21, no. 8 (April 15, 2001): 2706–15. http://dx.doi.org/10.1128/mcb.21.8.2706-2715.2001.

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ABSTRACT The UvsW protein of bacteriophage T4 is involved in many aspects of phage DNA metabolism, including repair, recombination, and recombination-dependent replication. UvsW has also been implicated in the repression of origin-dependent replication at late times of infection, when UvsW is normally synthesized. Two well-characterized T4 origins, ori(uvsY) andori(34), are believed to initiate replication through an R-loop mechanism. Here we provide both in vivo and in vitro evidence that UvsW is an RNA-DNA helicase that catalyzes the dissociation of RNA from origin R-loops. Two-dimensional gel analyses show that the replicative intermediates formed atori(uvsY) persist longer in a uvsWmutant infection than in a wild-type infection. In addition, the inappropriate early expression of UvsW protein results in the loss of these replicative intermediates. Using a synthetic origin R-loop, we also demonstrate that purified UvsW functions as a helicase that efficiently dissociates RNA from R-loops. These and previous results from a number of studies provide strong evidence that UvsW is a molecular switch that allows T4 replication to progress from a mode that initiates from R-loops at origins to a mode that initiates from D-loops formed by recombination proteins.

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Parker, Monica M., Maureen Belisle, and Marlene Belfort. "Intron Homing With Limited Exon Homology: Illegitimate Double-Strand-Break Repair in Intron Acquisition by Phage T4." Genetics 153, no. 4 (December 1, 1999): 1513–23. http://dx.doi.org/10.1093/genetics/153.4.1513.

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Abstract The td intron of bacteriophage T4 encodes a DNA endonuclease that initiates intron homing to cognate intronless alleles by a double-strand-break (DSB) repair process. A genetic assay was developed to analyze the relationship between exon homology and homing efficiency. Because models predict exonucleolytic processing of the cleaved recipient leading to homologous strand invasion of the donor allele, the assay was performed in wild-type and exonuclease-deficient (rnh or dexA) phage. Efficient homing was supported by exon lengths of 50 bp or greater, whereas more limited exon lengths led to a precipitous decline in homing levels. However, extensive homology in one exon still supported elevated homing levels when the other exon was completely absent. Analysis of these “one-sided” events revealed recombination junctions at ectopic sites of microhomology and implicated nucleolytic degradation in illegitimate DSB repair in T4. Interestingly, homing efficiency with extremely limiting exon homology was greatly elevated in phage deficient in the 3′-5′ exonuclease, DexA, suggesting that the length of 3′ tails is a major determinant of the efficiency of DSB repair. Together, these results suggest that illegitimate DSB repair may provide a means by which introns can invade ectopic sites.

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Mosig, Gisela. "BACTERIOPHAGE T4 GENE 32 PARTICIPATES IN EXCISION REPAIR AS WELL AS RECOMBINATIONAL REPAIR OF UV DAMAGES." Genetics 110, no. 2 (June 1, 1985): 159–71. http://dx.doi.org/10.1093/genetics/110.2.159.

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ABSTRACT Gene 32 of phage T4 has been shown previously to be involved in recombinational repair of UV damages but, based on a mutant study, was thought not to be required for excision repair. However, a comparison of UV-inactivation curves of several gene 32 mutants grown under conditions permissive for progeny production in wild-type or polA - hosts demonstrates that gene 32 participates in both kinds of repair. Different gene 32 mutations differentially inactivate these repair functions. Under conditions permissive for DNA replication and progeny production, all gene 32 mutants investigated here are partially defective in recombinational repair, whereas only two of them, P7 and P401, are also defective in excision repair. P401 is the only mutant whose final slope of the inactivation curve is significantly steeper than that of wildtype T4. These results are discussed in terms of interactions of gp32, a single-stranded DNA-binding protein, with DNA and with other proteins.

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Hinton, Deborah M., Suchira Pande, Neelowfar Wais, Xanthia B. Johnson, Madhavi Vuthoori, Anna Makela, and India Hook-Barnard. "Transcriptional takeover by σ appropriation: remodelling of the σ 70 subunit of Escherichia coli RNA polymerase by the bacteriophage T4 activator MotA and co-activator AsiA." Microbiology 151, no. 6 (June 1, 2005): 1729–40. http://dx.doi.org/10.1099/mic.0.27972-0.

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Activation of bacteriophage T4 middle promoters, which occurs about 1 min after infection, uses two phage-encoded factors that change the promoter specificity of the host RNA polymerase. These phage factors, the MotA activator and the AsiA co-activator, interact with the σ 70 specificity subunit of Escherichia coli RNA polymerase, which normally contacts the −10 and −35 regions of host promoter DNA. Like host promoters, T4 middle promoters have a good match to the canonical σ 70 DNA element located in the −10 region. However, instead of the σ 70 DNA recognition element in the promoter's −35 region, they have a 9 bp sequence (a MotA box) centred at −30, which is bound by MotA. Recent work has begun to provide information about the MotA/AsiA system at a detailed molecular level. Accumulated evidence suggests that the presence of MotA and AsiA reconfigures protein–DNA contacts in the upstream promoter sequences, without significantly affecting the contacts of σ 70 with the −10 region. This type of activation, which is called ‘σ appropriation’, is fundamentally different from other well-characterized models of prokaryotic activation in which an activator frequently serves to force σ 70 to contact a less than ideal −35 DNA element. This review summarizes the interactions of AsiA and MotA with σ 70, and discusses how these interactions accomplish the switch to T4 middle promoters by inhibiting the typical contacts of the C-terminal region of σ 70, region 4, with the host −35 DNA element and with other subunits of polymerase.

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Ciacci, Nagaia, Marco D’Andrea, Pasquale Marmo, Elisa Demattè, Francesco Amisano, Vincenzo Pilato, Maurizio Fraziano, Pietro Lupetti, Gian Rossolini, and Maria Thaller. "Characterization of vB_Kpn_F48, a Newly Discovered Lytic Bacteriophage for Klebsiella pneumoniae of Sequence Type 101." Viruses 10, no. 9 (September 9, 2018): 482. http://dx.doi.org/10.3390/v10090482.

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Resistance to carbapenems in Enterobacteriaceae, including Klebsiella pneumoniae, represents a major clinical problem given the lack of effective alternative antibiotics. Bacteriophages could provide a valuable tool to control the dissemination of antibiotic resistant isolates, for the decolonization of colonized individuals and for treatment purposes. In this work, we have characterized a lytic bacteriophage, named vB_Kpn_F48, specific for K. pneumoniae isolates belonging to clonal group 101. Phage vB_Kpn_F48 was classified as a member of Myoviridae, order Caudovirales, on the basis of transmission electron microscopy analysis. Physiological characterization demonstrated that vB_Kpn_F48 showed a narrow host range, a short latent period, a low burst size and it is highly stable to both temperature and pH variations. High throughput sequencing and bioinformatics analysis revealed that the phage is characterized by a 171 Kb dsDNA genome that lacks genes undesirable for a therapeutic perspective such integrases, antibiotic resistance genes and toxin encoding genes. Phylogenetic analysis suggests that vB_Kpn_F48 is a T4-like bacteriophage which belongs to a novel genus within the Tevenvirinae subfamily, which we tentatively named “F48virus”. Considering the narrow host range, the genomic features and overall physiological parameters phage vB_Kpn_F48 could be a promising candidate to be used alone or in cocktails for phage therapy applications.

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Spínola-Amilibia, Mercedes, Irene Davó-Siguero, Federico M. Ruiz, Elena Santillana, Francisco Javier Medrano, and Antonio Romero. "The structure of VgrG1 fromPseudomonas aeruginosa, the needle tip of the bacterial type VI secretion system." Acta Crystallographica Section D Structural Biology 72, no. 1 (January 1, 2016): 22–33. http://dx.doi.org/10.1107/s2059798315021142.

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The type VI secretion system (T6SS) is a mechanism that is commonly used by pathogenic bacteria to infect host cells and for survival in competitive environments. This system assembles on a core baseplate and elongates like a phage puncturing device; it is thought to penetrate the target membrane and deliver effectors into the host or competing bacteria. Valine–glycine repeat protein G1 (VgrG1) forms the spike at the tip of the elongating tube formed by haemolysin co-regulated protein 1 (Hcp1); it is structurally similar to the T4 phage (gp27)3–(gp5)3puncturing complex. Here, the crystal structure of full-length VgrG1 fromPseudomonas aeruginosais reported at a resolution of 2.0 Å, which through a trimeric arrangement generates a needle-like shape composed of two main parts, the head and the spike, connectedviaa small neck region. The structure reveals several remarkable structural features pointing to the possible roles of the two main segments of VgrG1: the head as a scaffold cargo domain and the β-roll spike with implications in the cell-membrane puncturing process and as a carrier of cognate toxins.

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Wang, Jun, and Joseph McGuire. "Surface Tension Kinetics of the Wild Type and Four Synthetic Stability Mutants of T4 Phage Lysozyme at the Air–Water Interface." Journal of Colloid and Interface Science 185, no. 2 (January 1997): 317–23. http://dx.doi.org/10.1006/jcis.1996.4619.

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Krasnykh, Victor, Natalya Belousova, Nikolay Korokhov, Galina Mikheeva, and David T. Curiel. "Genetic Targeting of an Adenovirus Vector via Replacement of the Fiber Protein with the Phage T4 Fibritin." Journal of Virology 75, no. 9 (May 1, 2001): 4176–83. http://dx.doi.org/10.1128/jvi.75.9.4176-4183.2001.

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ABSTRACT The utility of adenovirus (Ad) vectors for gene therapy is restricted by their inability to selectively transduce disease-affected tissues. This limitation may be overcome by the derivation of vectors capable of interacting with receptors specifically expressed in the target tissue. Previous attempts to alter Ad tropism by genetic modification of the Ad fiber have had limited success due to structural conflicts between the fiber and the targeting ligand. Here we present a strategy to derive an Ad vector with enhanced targeting potential by a radical replacement of the fiber protein in the Ad capsid with a chimeric molecule containing a heterologous trimerization motif and a receptor-binding ligand. Our approach, which capitalized upon the overall structural similarity between the human Ad type 5 (Ad5) fiber and bacteriophage T4 fibritin proteins, has resulted in the generation of a genetically modified Ad5 incorporating chimeric fiber-fibritin proteins targeted to artificial receptor molecules. Gene transfer studies employing this novel viral vector have demonstrated its capacity to efficiently deliver a transgene payload to the target cells in a receptor-specific manner.

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Hong, George, and Kenneth N. Kreuzer. "An Antitumor Drug-Induced Topoisomerase Cleavage Complex Blocks a Bacteriophage T4 Replication Fork In Vivo." Molecular and Cellular Biology 20, no. 2 (January 15, 2000): 594–603. http://dx.doi.org/10.1128/mcb.20.2.594-603.2000.

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ABSTRACT Many antitumor and antibacterial drugs inhibit DNA topoisomerases by trapping covalent enzyme-DNA cleavage complexes. Formation of cleavage complexes is important for cytotoxicity, but evidence suggests that cleavage complexes themselves are not sufficient to cause cell death. Rather, active cellular processes such as transcription and/or replication are probably necessary to transform cleavage complexes into cytotoxic lesions. Using defined plasmid substrates and two-dimensional agarose gel analysis, we examined the collision of an active replication fork with an antitumor drug-trapped cleavage complex. Discrete DNA molecules accumulated on the simple Y arc, with branch points very close to the topoisomerase cleavage site. Accumulation of the Y-form DNA required the presence of a topoisomerase cleavage site, the antitumor drug, the type II topoisomerase, and a T4 replication origin on the plasmid. Furthermore, all three arms of the Y-form DNA were replicated, arguing strongly that these are trapped replication intermediates. The Y-form DNA appeared even in the absence of two important phage recombination proteins, implying that Y-form DNA is the result of replication rather than recombination. This is the first direct evidence that a drug-induced topoisomerase cleavage complex blocks the replication fork in vivo. Surprisingly, these blocked replication forks do not contain DNA breaks at the topoisomerase cleavage site, implying that the replication complex was inactivated (at least temporarily) and that topoisomerase resealed the drug-induced DNA breaks. The replication fork may behave similarly at other types of DNA lesions, and thus cleavage complexes could represent a useful (site-specific) model for chemical- and radiation-induced DNA damage.

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Kutter, Elizabeth, Ketevan Gachechiladze, Alexandr Poglazov, Elena Marusich, Mikhail Shneider, Pia Aronsson, Alberto Napuli, Darlene Porter, and Vadim Mesyanzhinov. "Evolution of T4-related phages." Virus Genes 11, no. 2-3 (June 1995): 285–97. http://dx.doi.org/10.1007/bf01728666.

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Journal articles on the topic 'Phages de type T4'

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