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Andrew M Kropinski - One of the best experts on this subject based on the ideXlab platform.
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sequence genome organization annotation and proteomics of the thermophilic 47 7 kb geobacillus stearothermophilus bacteriophage tp 84 and its classification in the new tp84virus genus
PLOS ONE, 2018Co-Authors: Piotr M Skowron, Andrew M Kropinski, Joanna Zebrowska, Lukasz Janus, Kasjan Szemiako, Edyta Czajkowska, Natalia Maciejewska, Malgorzata Skowron, Joanna M łoś, Marcin łośAbstract:Bacteriophage TP-84 is a well-characterized bacteriophage of historical interest. It is a member of the Siphoviridae, and infects a number of thermophilic Geobacillus (Bacillus) stearothermophilus strains. Its' 47.7-kbp double-stranded DNA genome revealed the presence of 81 coding sequences (CDSs) coding for polypeptides of 4 kDa or larger. Interestingly, all CDSs are oriented in the same direction, pointing to a dominant transcription direction of one DNA strand. Based on a homology search, a hypothetical function could be assigned to 31 CDSs. No RNA or DNA polymerase-coding genes were found on the bacteriophage genome indicating that TP-84 relies on the host's transcriptional and replication enzymes. The TP84 genome is tightly packed with CDSs, typically spaced by several-to-tens of bp or often overlapping. The genome contains five putative promoter-like sequences showing similarity to the host promoter consensus sequence and allowing for a 2-bp mismatch. In addition, ten putative rho-independent terminators were detected. Because the genome sequence shows essentially no similarity to any previously characterised bacteriophage, TP-84 should be considered a new species in an undefined genus within the Siphoviridae family. Thus a taxonomic proposal of a new Tp84virus genus has been accepted by the International Committee on Taxonomy of Viruses. The bioinformatics genome analysis was verified by confirmation of 33 TP-84 proteins, which included: a) cloning of a selected CDS in Escherichia coli, coding for a DNA single-stranded binding protein (SSB; gene TP84_63), b) purification and functional assays of the recombinant TP-84 SSB, which has been shown to improve PCR reactions, c) mass spectrometric (MS) analysis of TP-84 bacteriophage capsid proteins, d) purification of TP-84 endolysin activity, e) MS analysis of the host cells from infection time course.
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Genome Sequence of vB_AbaS_TRS1, a Viable Prophage Isolated from Acinetobacter baumannii Strain A118
Genome Announcements, 2016Co-Authors: Dann Turner, Andrew M Kropinski, Matthew E. Wand, J. Mark Sutton, Daniela Centrón, Darren M. ReynoldsAbstract:© 2016 Turner et al. A novel temperate phage, vB_AbaS_TRS1, was isolated from cultures of Acinetobacter baumannii strain A118 that had been exposed to mitomycin C. Phage TRS1 belongs to the Siphoviridae family of bacteriophages and encapsulates a 40,749-bp genome encoding 70 coding sequences and a single tRNA.
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integration of genomic and proteomic analyses in the classification of the Siphoviridae family
Virology, 2015Co-Authors: Evelien M Adriaenssens, Andrew M Kropinski, Hans-wolfgang Ackermann, Robert P Edwards, John H E Nash, Padmanabhan Mahadevan, Donald Seto, Rob LavigneAbstract:Abstract Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae . In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera ( Phic3unalikevirus; L5likevirus ) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.
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Characterization of Staphylococcus epidermidis phage vB_SepS_SEP9 : a unique member of the Siphoviridae family
Research in Microbiology, 2014Co-Authors: Luís D. R. Melo, Andrew M Kropinski, Hans-wolfgang Ackermann, Joana Azeredo, Sanna Sillankorva, Nuno CercaAbstract:Relatively few phages (
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characterization of staphylococcus epidermidis phage vb_seps_sep9 a unique member of the Siphoviridae family
Research in Microbiology, 2014Co-Authors: Luís D. R. Melo, Andrew M Kropinski, Hans-wolfgang Ackermann, Joana Azeredo, Sanna Sillankorva, Nuno CercaAbstract:Relatively few phages (<10) of coagulase negative staphylococci (CoNS) have been described. Staphylococcus epidermidis phage vB_SepS_SEP9 is a siphovirus with a unique morphology as a staphylococcal phage, possessing a very long tail. Its genome is unique and unrelated to any phage genomes deposited in public databases. It appears to encode a nonfunctional integrase. Due to the not having a recognizable lysogeny module, the phage is unable lysogenize. The genome comprises 129 coding sequences (CDS), 46 of which have an assigned function and 59 are unique. Its unique morphology and genome led to the proposal of the establishment of a new Siphoviridae genus named “Sep9likevirus”.
Douwe Van Sinderen - One of the best experts on this subject based on the ideXlab platform.
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comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages
Scientific Reports, 2016Co-Authors: James Murphy, Horst Neve, Jennifer Mahony, Francesca Bottacini, Philip Kelleher, Aldert Zomer, Arjen Nauta, Douwe Van SinderenAbstract:Genome sequencing and comparative analysis of bacteriophage collections has greatly enhanced our understanding regarding their prevalence, phage-host interactions as well as the overall biodiversity of their genomes. This knowledge is very relevant to phages infecting Lactococcus lactis, since they constitute a significant risk factor for dairy fermentations. Of the eighty four lactococcal phage genomes currently available, fifty five belong to the so-called 936 group, the most prevalent of the ten currently recognized lactococcal phage groups. Here, we report the genetic characteristics of a new collection of 936 group phages. By combining these genomes to those sequenced previously we determined the core and variable elements of the 936 genome. Genomic variation occurs across the 936 phage genome, such as genetic elements that (i) lead to a +1 translational frameshift resulting in the formation of additional structures on the phage tail, (ii) specify a double neck passage structure, and (iii) encode packaging module-associated methylases. Hierarchical clustering of the gene complement of the 936 group phages and nucleotide alignments allowed grouping of the ninety 936 group phages into distinct clusters, which in general appear to correspond with their geographical origin.
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lactococcus lactis phage tp901 1 as a model for Siphoviridae virion assembly
Bacteriophage, 2016Co-Authors: Jennifer Mahony, Stephen R. Stockdale, Barry Collins, François P. Douillard, Christian Cambillau, S Spinelli, Douwe Van SinderenAbstract:ABSTRACTPhages infecting Lactococcus lactis pose a serious threat to the dairy fermentation sector. Consequently, they are among the most thoroughly characterized Gram positive-infecting phages. The majority of lactococcal phages belong to the tailed family of phages named the Siphoviridae. The coliphage lambda and the Bacillus subtilis phage SPP1 have been the predominant comparators for emerging siphophages both genomically and structurally and both phages recognize a membrane protein receptor. In contrast, the lactococcal P335 group phage TP901-1 attaches to cell wall surface polysaccharides. It is a typical “lambdoid” siphophage possessing a long non-contractile tail and a genomic architecture reminiscent of lambda and SPP1 despite low or undetectable sequence homology in many of its encoded products, especially those involved in host recognition. A functional analysis of the structural components of TP901-1 was undertaken based on the characterization of a series of mutants in the region encoding the...
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Structure and Assembly of TP901-1 Virion Unveiled by Mutagenesis
PLOS ONE, 2015Co-Authors: Stephen R. Stockdale, Barry Collins, Silvia Spinelli, François P. Douillard, Jennifer Mahony, Christian Cambillau, Douwe Van SinderenAbstract:Bacteriophages of the Siphoviridae family represent the most abundant viral morphology in the biosphere, yet many molecular aspects of their virion structure, assembly and associated functions remain to be unveiled. In this study, we present a comprehensive mutational and molecular analysis of the temperate Lactococcus lactis-infecting phage TP901-1. Fourteen mutations located within the structural module of TP901-1 were created; twelve mutations were designed to prevent full length translation of putative proteins by non-sense mutations, while two additional mutations caused aberrant protein production. Electron microscopy and Western blot analysis of mutant virion preparations, as well as in vitro assembly of phage mutant combinations, revealed the essential nature of many of the corresponding gene products and provided information on their biological function(s). Based on the information obtained, we propose a functional and assembly model of the TP901-1 Siphoviridae virion.
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genome analysis of the clostridium difficile phage φcd6356 a temperate phage of the Siphoviridae family
Gene, 2010Co-Authors: Marianne Horgan, Gerald F. Fitzgerald, Douwe Van Sinderen, Orla Osullivan, Aidan Coffey, Olivia Mcauliffe, Paul R RossAbstract:Abstract The temperate phages ΦCD6356 and ΦCD6365 were isolated and characterised following mitomycin C induction of 43 Clostridium difficile strains. Both phages belong to the Siphoviridae family and have genome sizes of 37,664 bp for ΦCD6356 based on sequence data and approximately 50 kb for ΦCD6365 based on restriction analysis. Protein analysis revealed similar protein profiles and indicated posttranslational processing of the ΦCD6356 major capsid protein. The genome sequence of ΦCD6356 is substantially different from other previously reported phage sequences and a putative function could be assigned to only 21 out of 59 predicted open reading frames. However, the genome organisation closely resembles that of other members of the Siphoviridae family which infect low GC-content Gram-positive bacteria. The modular organisation, genome synteny, presence of cohesive ends and posttranslational processing of the capsid protein suggest ΦCD6356 is a member of the proposed Sfi21-like genera. To our knowledge, this report represents the first C. difficile phage of the Siphoviridae family to be sequenced.
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Genome analysis of the Clostridium difficile phage PhiCD6356, a temperate phage of the Siphoviridae family.
Gene, 2010Co-Authors: Marianne Horgan, Gerald F. Fitzgerald, Douwe Van Sinderen, Aidan Coffey, Olivia Mcauliffe, Orla O'sullivan, R Paul RossAbstract:The temperate phages PhiCD6356 and PhiCD6365 were isolated and characterised following mitomycin C induction of 43 Clostridium difficile strains. Both phages belong to the Siphoviridae family and have genome sizes of 37,664 bp for PhiCD6356 based on sequence data and approximately 50 kb for PhiCD6365 based on restriction analysis. Protein analysis revealed similar protein profiles and indicated posttranslational processing of the PhiCD6356 major capsid protein. The genome sequence of PhiCD6356 is substantially different from other previously reported phage sequences and a putative function could be assigned to only 21 out of 59 predicted open reading frames. However, the genome organisation closely resembles that of other members of the Siphoviridae family which infect low GC-content Gram-positive bacteria. The modular organisation, genome synteny, presence of cohesive ends and posttranslational processing of the capsid protein suggest PhiCD6356 is a member of the proposed Sfi21-like genera. To our knowledge, this report represents the first C. difficile phage of the Siphoviridae family to be sequenced.
Steve Petrovski - One of the best experts on this subject based on the ideXlab platform.
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the varying effects of a range of preservatives on myoviridae and Siphoviridae bacteriophages formulated in a semi solid cream preparation
Letters in Applied Microbiology, 2020Co-Authors: Steve Petrovski, Teagan L. Brown, Heng Ku, George Mnatzaganian, Michael J Angove, Mwila Kabwe, Joseph TucciAbstract:: Bacteriophages may be formulated into semi-solid bases for therapeutic delivery. This work investigated the effects of a range of preservatives on the viability of Myoviridae and Siphoviridae bacteriophages when these were formulated into a standard semi-solid cream base. The six preservatives tested included: benzoic acid (0.1%), chlorocresol (0.1%), combination hydroxybenzoates (propyl 4-hydroxybenzoates with methyl 4-hydroxybenzoates) (0.1%), methyl 4-hydroxybenzoate (0.08%), 2-phenoxyethanol (1%), and propyl 4-hydroxybenzoate (0.02%). These were each formulated into cetomacrogol cream aqueous to generate six individual semi-solid bases into which Myoviridae and Siphoviridae bacteriophages were added and tested for stability. Optimal bacteriophage stability was seen when the preservative chlorocresol was used. Bacteriophage in the acidic benzoic acid were the least stable, resulting in complete loss of viability after four to five weeks. Of the bacteriophages tested, the Myoviridae KOX1 was significantly more stable than the Siphoviridae PAC1 after 91 days in formulations with each of the preservatives. Our results suggest the need for individual testing of specific bacteriophages in pharmaceutical formulations, as their efficacy when exposed to preservatives and excipients in these delivery forms may vary.
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The varying effects of a range of preservatives on Myoviridae and Siphoviridae bacteriophages formulated in a semi‐solid cream preparation
Letters in Applied Microbiology, 2020Co-Authors: Teagan L. Brown, Steve Petrovski, Heng Ku, George Mnatzaganian, Michael J Angove, Mwila Kabwe, Joseph TucciAbstract:: Bacteriophages may be formulated into semi-solid bases for therapeutic delivery. This work investigated the effects of a range of preservatives on the viability of Myoviridae and Siphoviridae bacteriophages when these were formulated into a standard semi-solid cream base. The six preservatives tested included: benzoic acid (0.1%), chlorocresol (0.1%), combination hydroxybenzoates (propyl 4-hydroxybenzoates with methyl 4-hydroxybenzoates) (0.1%), methyl 4-hydroxybenzoate (0.08%), 2-phenoxyethanol (1%), and propyl 4-hydroxybenzoate (0.02%). These were each formulated into cetomacrogol cream aqueous to generate six individual semi-solid bases into which Myoviridae and Siphoviridae bacteriophages were added and tested for stability. Optimal bacteriophage stability was seen when the preservative chlorocresol was used. Bacteriophage in the acidic benzoic acid were the least stable, resulting in complete loss of viability after four to five weeks. Of the bacteriophages tested, the Myoviridae KOX1 was significantly more stable than the Siphoviridae PAC1 after 91 days in formulations with each of the preservatives. Our results suggest the need for individual testing of specific bacteriophages in pharmaceutical formulations, as their efficacy when exposed to preservatives and excipients in these delivery forms may vary.
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Isolation and characterization of bacteriophage NTR1 infectious for Nocardia transvalensis and other Nocardia species.
Virus Genes, 2018Co-Authors: Stephanie Taylor, Robert J. Seviour, Teagan L. Brown, Joseph Tucci, Peter Lock, Steve PetrovskiAbstract:: We describe here the isolation and characterization of the bacteriophage, NTR1 from activated sludge. This phage is lytic for Nocardia transvalensis, Nocardia brasiliensis and Nocardia farcinica. NTR1 phage has a genome sequence of 65,275 bp in length, and its closest match is to the Skermania piniformis phage SPI1 sharing over 36% of its genome. The phage belongs to the Siphoviridae family, possessing a long non-contractile tail and icosahedral head. Annotation of the genome reveals 97 putative open reading frames arranged in the characteristic modular organization of Siphoviridae phages and contains a single tRNA-Met gene.
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Lysis to Kill: Evaluation of the Lytic Abilities, and Genomics of Nine Bacteriophages Infective for Gordonia spp. and Their Potential Use in Activated Sludge Foam Biocontrol
PLOS ONE, 2015Co-Authors: Zoe A Dyson, Robert J. Seviour, Joseph Tucci, Steve PetrovskiAbstract:Nine bacteriophages (phages) infective for members of the genus Gordonia were isolated from wastewater and other natural water environments using standard enrichment techniques. The majority were broad host range phages targeting more than one Gordonia species. When their genomes were sequenced, they all emerged as double stranded DNA Siphoviridae phages, ranging from 17,562 to 103,424 bp in size, and containing between 27 and 127 genes, many of which were detailed for the first time. Many of these phage genomes diverged from the expected modular genome architecture of other characterized Siphoviridae phages and contained unusual lysis gene arrangements. Whole genome sequencing also revealed that infection with lytic phages does not appear to prevent spontaneous prophage induction in Gordonia malaquae lysogen strain BEN700. TEM sample preparation techniques were developed to view both attachment and replication stages of phage infection.
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Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4
Applied and Environmental Microbiology, 2015Co-Authors: Zoe A Dyson, Robert J. Seviour, Joseph Tucci, Steve PetrovskiAbstract:Three Tsukamurella phages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of these Siphoviridae viruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously described Gordonia phage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture of Siphoviridae phages. All three phages appeared highly virulent on strains of Tsukamurella inchonensis and Tsukamurella paurometabola.
Harald Brüssow - One of the best experts on this subject based on the ideXlab platform.
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The prophage sequences of Lactobacillus plantarum strain WCFS1.
Virology, 2003Co-Authors: Marco Ventura, Carlos Canchaya, Michiel Kleerebezem, Roland J. Siezen, Harald BrüssowAbstract:Abstract The Lactobacillus plantarum commensal WCFS1 contains four prophage elements in its genome. Lp1 and Lp2 are two about 40-kb-long uninducible prophages that share closely related DNA packaging, head and tail genes defining a second lineage of pac -site Siphoviridae in L. plantarum, distinct from L. plantarum phage phig1e, but related to Bacillus phage SPP1 and Lactococcus phage TP901-1. Northern analysis revealed transcribed prophage genes exclusively near both attachment sites. Comparative genomics identified candidate lysogenic conversion genes (LCG) downstream of the lysis cassette and within the lysogeny module. Notable are genes with sequence similarities to putative LCG from Streptococcus pyogenes prophages and to a Bacillus plasmid. Both prophages harbored tRNA genes. R-Lp3 and R-Lp4 represent short prophage remnants; R-Lp3 abuts Lp2 and displays sequence links to cos -site Siphoviridae.
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Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved.
Trends in microbiology, 2002Co-Authors: E. Fidelma Boyd, Harald BrüssowAbstract:There are common themes among bacteriophage-encoded virulence factors, which include the well-characterized bacterial toxins and proteins that alter antigenicity as well as several new classes of bacteriophage-encoded proteins such as superantigens, effectors translocated by a type III secretion system, and proteins required for intracellular survival and host cell attachment. These virulence factors are encoded by a diversity of bacteriophages, members of the viral families Siphoviridae, Podoviridae, Myoviridae and Inoviridae, with some bacteriophages having characteristics of more than one virus family. The location of virulence genes within the bacteriophage genomes is non-random and consistent with an origin via imprecise prophage excision or as either transferable cassettes or integral components of the bacteriophage genome.
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comparative phage genomics and the evolution of Siphoviridae insights from dairy phages
Molecular Microbiology, 2001Co-Authors: Harald Brüssow, Frank DesiereAbstract:Comparative phage genomics can retrace part of the evolutionary history of phage modules encoding phage-specific functions such as capsid building or establishment of the lysogenic state. The diagnosis of relatedness is not based exclusively on sequence similarity, but includes topological considerations of genome organization. The gene maps from the λ-, ψM2-, L5-, Sfi21-, Sfi11-, φC31-, sk1- and TM4-like phages showed a remarkable synteny of their structural genes defining a λ supergroup within Siphoviridae (Caudovirales with long non-contractile tails). A hierarchy of relatedness within the λ supergroup suggested elements of vertical evolution in the capsid module of Siphoviridae. Links to P22-like Podoviridae and P2-like Myoviridae were also detected. Numerous cases of horizontal gene transfer were observed, but recent transfers were limited to interbreeding phage populations. We suggest that tailed phages are the result of both vertical and horizontal evolution and are thus a good model system for web-like phylogenies.
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similarly organized lysogeny modules in temperate Siphoviridae from low gc content gram positive bacteria
Virology, 1999Co-Authors: Sacha Lucchini, Frank Desiere, Harald BrüssowAbstract:Temperate Siphoviridae from an evolutionarily related branch of low GC content gram-positive bacteria share a common genetic organization of lysogeny-related genes and the predicted proteins are linked by many sequence similarities. Their compact lysogeny modules [integrase/1–2 orfs (phage exclusion? and metalloproteinase motif proteins)/cI-like repressor/cro-like repressor/antirepressor (optional)] differ clearly from that of λ-like and L5-like viruses, the two currently established genera of temperate Siphoviridae, while they resemble those of the P2-like genus of Myoviridae. In all known temperate Siphoviridae from low GC content gram-positive bacteria the lysogeny module is flanked by the lysis module and the DNA replication module. This modular organization is again distinct from that of the known genera of temperate Siphoviridae. On the basis of comparative sequence analysis we propose a new genus of Siphoviridae: “Sfi21-like” phages. With a larger database of phage sequences it might be possible to establish a genomics-based phage taxonomy and to retrace the evolutionary history of selected phage modules or individual phage genes. The antirepressor of Sfi21-like phages has an unusual widespread distribution since proteins with high aa similarity (40%) were found not only in phages from gram-negative bacteria, but also in insect viruses.
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the structural gene module instreptococcus thermophilusbacteriophage φsfi11 shows a hierarchy of relatedness to Siphoviridae from a wide range of bacterial hosts
Virology, 1998Co-Authors: Sacha Lucchini, Frank Desiere, Harald BrüssowAbstract:Abstract The structural gene cluster and the lysis module from lytic group II Streptococcus thermophilus bacteriophage φSfi11 was compared to the corresponding region from other Siphoviridae. The analysis revealed a hierarchy of relatedness. φSfi11 differed from the temperate S. thermophilus bacteriophage φO1205 by about 10% at the nucleotide level. The majority of the changes were point mutations, mainly at the third base position. Only a single gene (orf 695) differed substantially between the two phages. Over the putative minor tail and lysis genes, φSfi11 and the lytic group I S. thermophilus φSfi19 shared regions with variable degrees of similarity. Orf 1291 from φSfi19 was replaced by four genes in φSfi11, two of which (orf 1000 and orf 695) showed a complicated pattern of similarity and nonsimilarity compared with φSfi19. The predicted orf 695 gp resembles the receptor-recognizing protein of T-even coliphages in its organization, but not its sequence. No sequence similarity was detected between φSfi11 and φSfi19 in the region covering the major head and tail genes. Comparison of the structural gene map of φSfi11 with that of Siphoviridae from gram-positive and -negative bacterial hosts revealed a common genomic organization. Sequence similarity was only found between φSfi11 and Siphoviridae from gram-positive hosts and correlated with the evolutionary distance between the bacterial hosts. Our data are compatible with the hypothesis that the structural gene operon from Siphoviridae of the low G+C group of gram-positive bacteria is derived from a common ancestor.
Nuno Cerca - One of the best experts on this subject based on the ideXlab platform.
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Characterization of Staphylococcus epidermidis phage vB_SepS_SEP9 : a unique member of the Siphoviridae family
Research in Microbiology, 2014Co-Authors: Luís D. R. Melo, Andrew M Kropinski, Hans-wolfgang Ackermann, Joana Azeredo, Sanna Sillankorva, Nuno CercaAbstract:Relatively few phages (
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characterization of staphylococcus epidermidis phage vb_seps_sep9 a unique member of the Siphoviridae family
Research in Microbiology, 2014Co-Authors: Luís D. R. Melo, Andrew M Kropinski, Hans-wolfgang Ackermann, Joana Azeredo, Sanna Sillankorva, Nuno CercaAbstract:Relatively few phages (<10) of coagulase negative staphylococci (CoNS) have been described. Staphylococcus epidermidis phage vB_SepS_SEP9 is a siphovirus with a unique morphology as a staphylococcal phage, possessing a very long tail. Its genome is unique and unrelated to any phage genomes deposited in public databases. It appears to encode a nonfunctional integrase. Due to the not having a recognizable lysogeny module, the phage is unable lysogenize. The genome comprises 129 coding sequences (CDS), 46 of which have an assigned function and 59 are unique. Its unique morphology and genome led to the proposal of the establishment of a new Siphoviridae genus named “Sep9likevirus”.
