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Minna M. Poranen - One of the best experts on this subject based on the ideXlab platform.
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Microbial production of lipid-protein vesicles using enveloped bacterioPhage phi6
Microbial Cell Factories, 2019Co-Authors: Outi L. Lyytinen, Daria Starkova, Minna M. PoranenAbstract:Background Cystoviruses have a phospholipid envelope around their nucleocapsid. Such a feature is unique among bacterial viruses (i.e., bacterioPhages) and the mechanisms of virion envelopment within a bacterial host are largely unknown. The cystovirus Pseudomonas Phage phi6 has an envelope that harbors five viral membrane proteins and phospholipids derived from the cytoplasmic membrane of its Gram-negative host. The phi6 major envelope protein P9 and the non-structural protein P12 are essential for the envelopment of its virions. Co-expression of P9 and P12 in a Pseudomonas host results in the formation of intracellular vesicles that are potential intermediates in the phi6 virion assembly pathway. This study evaluated the minimum requirements for the formation of phi6-specific vesicles and the possibility to localize P9-tagged heterologous proteins into such structures in Escherichia coli . Results Using transmission electron microscopy, we detected membranous structures in the cytoplasm of E. coli cells expressing P9. The density of the P9-specific membrane fraction was lower (approximately 1.13 g/cm^3 in sucrose) than the densities of the bacterial cytoplasmic and outer membrane fractions. A P9-GFP fusion protein was used to study the targeting of heterologous proteins into P9 vesicles. Production of the GFP-tagged P9 vesicles required P12, which protected the fusion protein against proteolytic cleavage. Isolated vesicles contained predominantly P9-GFP, suggesting selective incorporation of P9-tagged fusion proteins into the vesicles. Conclusions Our results demonstrate that the phi6 major envelope protein P9 can trigger formation of cytoplasmic membrane structures in E. coli in the absence of any other viral protein. Intracellular membrane structures are rare in bacteria, thus making them ideal chasses for cell-based vesicle production. The possibility to locate heterologous proteins into the P9-lipid vesicles facilitates the production of vesicular structures with novel properties. Such products have potential use in biotechnology and biomedicine.
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Recognition of six additional cystoviruses: Pseudomonas virus phi6 is no longer the sole species of the family Cystoviridae
Archives of Virology, 2018Co-Authors: Sari Mäntynen, Lotta-riina Sundberg, Minna M. PoranenAbstract:Cystoviridae is a family of bacterial viruses (bacterioPhages) with a tri-segmented dsRNA genome. It includes a single genus Cystovirus , which has presently only one recognised virus species, Pseudomonas virus phi6 . However, a large number of additional dsRNA Phages have been isolated from various environmental samples, indicating that such viruses are more widespread and abundant than previously recognised. Six of the additional dsRNA Phage isolates (Pseudomonas Phages phi8, phi12, phi13, phi2954, phiNN and phiYY) have been fully sequenced. They all infect Pseudomonas species, primarily plant pathogenic Pseudomonas syringae strains. Due to the notable genetic and structural similarities with Pseudomonas Phage phi6, we propose that these viruses should be included into the Cystovirus genus (and consequently into the Cystoviridae family). Here, we present an updated taxonomy of the family Cystoviridae and give a short overview of the properties of the type member phi6 as well as the putative new members of the family.
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A list of virus species having RdRp structures in the PDB, observed non-catalytic ion types, and distances of non-catalytic ions from the catalytic site.
2012Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:1Abbreviations used: RHV, rabbit hemorrhagic virus; BVDV, bovine viral diarrhea virus; Qβ, enterobacteria virus Qβ; FMDV, foot-and-mouth disease virus; coxsackie virus, human enterovirus B; IBDV, infectious bursal disease virus; φ6, Pseudomonas Phage φ6; reovirus, mammalian orthoreovirus.2The viral species for which a non-catalytic metal was found are in bold.3PDBids are given only for structures that include a non-catalytic ion.4Structures used for the determination of the distances are in bold.5Structures were structurally aligned with the hepatitis C virus RdRp structure (PDBid: 2WHO). Distances were measured from catalytic ion A of the hepatitis C virus RdRp.
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The amino acid sequences of motifs A, C, and E from the structural alignment.
2012Co-Authors: Heli A. M. Mönttinen, Janne J. Ravantti, Minna M. PoranenAbstract:The number of the first residue in each motif is given. The amino acids that coordinate the catalytic ion are indicated with grey dots (below the alignment). The residues that coordinate the non-catalytic ion in different polymerases are marked with squares. Blue squares indicate that the amino acid coordinates the non-catalytic ion with its side chain, and red squares indicate that the main chain coordinates the ion. The names of the viral species and families are shown on the left. Abbreviations used: RHV, rabbit hemorrhagic virus; BVDV, bovine viral diarrhea virus; FMDV, foot-and-mouth disease virus; coxsackie virus, human enterovirus B; Qβ, enterobacteria virus Qβ; φ6, Pseudomonas Phage φ6; IBDV, infectious bursal disease virus; HIV, human immunodeficiency virus; and MLV, murine leukemia virus. The non-catalytic ion is observed in species marked with (*). The alignment is colored according to ClustalX 2.0.12 default settings [57].
Sari Mäntynen - One of the best experts on this subject based on the ideXlab platform.
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Recognition of six additional cystoviruses: Pseudomonas virus phi6 is no longer the sole species of the family Cystoviridae
Archives of Virology, 2018Co-Authors: Sari Mäntynen, Lotta-riina Sundberg, Minna M. PoranenAbstract:Cystoviridae is a family of bacterial viruses (bacterioPhages) with a tri-segmented dsRNA genome. It includes a single genus Cystovirus , which has presently only one recognised virus species, Pseudomonas virus phi6 . However, a large number of additional dsRNA Phages have been isolated from various environmental samples, indicating that such viruses are more widespread and abundant than previously recognised. Six of the additional dsRNA Phage isolates (Pseudomonas Phages phi8, phi12, phi13, phi2954, phiNN and phiYY) have been fully sequenced. They all infect Pseudomonas species, primarily plant pathogenic Pseudomonas syringae strains. Due to the notable genetic and structural similarities with Pseudomonas Phage phi6, we propose that these viruses should be included into the Cystovirus genus (and consequently into the Cystoviridae family). Here, we present an updated taxonomy of the family Cystoviridae and give a short overview of the properties of the type member phi6 as well as the putative new members of the family.
Azeredo Joana - One of the best experts on this subject based on the ideXlab platform.
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Complete genome sequence of the lytic Pseudomonas fluorescens Phage ϕIBB-PF7A
BMC, 2011Co-Authors: Kropinski Andrew M, Lingohr Erika J, Kluskens Leon D, Sillankorva Sanna, Neubauer Peter, Azeredo JoanaAbstract:Abstract Background Phage ϕIBB-PF7A is a T7-like bacterioPhage capable of infecting several Pseudomonas fluorescens dairy isolates and is extremely efficient in lysing this bacterium even when growing in biofilms attached to surfaces. This work describes the complete genome sequence of this Phage. Results The genome consists of a linear double-stranded DNA of 40,973 bp, with 985 bp long direct terminal repeats and a GC content of approximately 56%. There are 52 open reading frames which occupy 94.6% of the genome ranging from 137 to 3995 nucleotides. Twenty eight (46.7%) of the proteins encoded by this virus exhibit sequence similarity to coliPhage T7 proteins while 34 (81.0%) are similar to proteins of Pseudomonas Phage gh-1. Conclusions That this Phage is closely related to Pseudomonas putida Phage gh-1 and coliPhage T7 places it in the "T7-like viruses" genus of the subfamily Autographivirinae within the family Podoviridae. Compared to the genome of gh-1, the sequence of ϕIBB-PF7A is longer and contains more genes with unassigned function and lacks a few potentially essential and non-essential T7 genes, such as gene1.1, 3.8, and 7.
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Complete genome sequence of the lytic Pseudomonas fluorescens Phage ϕIBB-PF7A
'Springer Science and Business Media LLC', 2011Co-Authors: Sillankorva Sanna, Kropinski Andrew M, Kluskens Leon, Linghorn E., Neubauer P., Azeredo JoanaAbstract:Background Phage ϕIBB-PF7A is a T7-like bacterioPhage capable of infecting several Pseudomonas fluorescens dairy isolates and is extremely efficient in lysing this bacterium even when growing in biofilms attached to surfaces. This work describes the complete genome sequence of this Phage. Results The genome consists of a linear double-stranded DNA of 40,973 bp, with 985 bp long direct terminal repeats and a GC content of approximately 56%. There are 52 open reading frames which occupy 94.6% of the genome ranging from 137 to 3995 nucleotides. Twenty eight (46.7%) of the proteins encoded by this virus exhibit sequence similarity to coliPhage T7 proteins while 34 (81.0%) are similar to proteins of Pseudomonas Phage gh-1. Conclusions That this Phage is closely related to Pseudomonas putida Phage gh-1 and coliPhage T7 places it in the "T7-like viruses" genus of the subfamily Autographivirinae within the family Podoviridae. Compared to the genome of gh-1, the sequence of ϕIBB-PF7A is longer and contains more genes with unassigned function and lacks a few potentially essential and non-essential T7 genes, such as gene1.1, 3.8, and 7.SS acknowledges the financial support from the Portuguese Foundation for Science and Technology (FCT) (grant SFRH/BD/18485/2004). AK acknowledges the financial support of a discovery grant from the Natural Sciences and Engineering Research Council of Canada
Damian J. Magill - One of the best experts on this subject based on the ideXlab platform.
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Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacterioPhages.
PloS one, 2017Co-Authors: Damian J. Magill, Victor N. Krylov, John W. Mcgrath, Christopher C. R. Allen, John P. Quinn, O. V. Shaburova, Leonid KulakovAbstract:We present the analysis of two novel Pseudomonas putida Phages, pf16 and phiPMW. Pf16 represents a peripherally related T4-like Phage, and is the first of its kind infecting a Pseudomonad, with evidence suggesting cyanoPhage origins. Extensive divergence has resulted in pf16 occupying a newly defined clade designated as the pf16-related Phages, lying at the interface of the Schizo T-Evens and Exo T-Evens. Recombination with an ancestor of the P. putida Phage AF is likely responsible for the tropism of this Phage. phiPMW represents a completely novel Pseudomonas Phage with a genome containing substantial genetic novelty through its many hypothetical proteins. Evidence suggests that this Phage has been extensively shaped through gene transfer events and vertical evolution. Phylogenetics shows that this Phage has an evolutionary history involving FelixO1-related viruses but is in itself highly distinct from this group.
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Graph showing distribution of putative Tevenvirinae genome sizes.
2017Co-Authors: Damian J. Magill, Victor N. Krylov, Olga V. Shaburova, John W. Mcgrath, Christopher C. R. Allen, John P. Quinn, Leonid A. KulakovAbstract:Phages infecting related hosts are colour coded appropriately with labels provided specifying the Phage or group of Phages. Pseudomonas Phage pf16, Rhodothermus Phage RM378 (smallest genome), Prochlorococcus Phage P-SSM2 (largest genome), and Enterobacteria Phage T4 are circled and labelled in bold. Contour density lines shows clustering of most Phages around similar genome sizes. Boxplot at the bottom of the figure summarises the distribution of the Phages. The main box and associated lines shows the spread, mean, and quartiles of the main cluster observed within the major contour lines with outliers and the smallest/largest genomes represented as dots.
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Table showing sigma70 promoter elements within Pseudomonas Phage pf16.
2017Co-Authors: Damian J. Magill, Victor N. Krylov, Olga V. Shaburova, John W. Mcgrath, Christopher C. R. Allen, John P. Quinn, Leonid A. KulakovAbstract:Table showing sigma70 promoter elements within Pseudomonas Phage pf16.
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Analysis of Pseudomonas Phage pf16 stringent starvation protein B (SspB).
2017Co-Authors: Damian J. Magill, Victor N. Krylov, Olga V. Shaburova, John W. Mcgrath, Christopher C. R. Allen, John P. Quinn, Leonid A. KulakovAbstract:(a): Superimposition of Pseudomonas putida and pf16 SspB molecular models with resulting TM-align score of 0.818 indicating a high level of structural similarity. (b): Sequence alignment of P. putida and pf16 SspB proteins showing a high level of identity. Note the deletion in pf16 of numerous negatively charged residues (aspartate and glutamate). (c): Predicted complex between P. putida sigma factor RpoE, anti-sigma factor RseA, and both P. putida and pf16 SspB protein models highlighting the overlap in binding sites and thus putative competitive inhibitory action by pf16 SspB. The deletion in pf16 SspB compared to P. putida is highlighted in dark blue.
Lotta-riina Sundberg - One of the best experts on this subject based on the ideXlab platform.
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Recognition of six additional cystoviruses: Pseudomonas virus phi6 is no longer the sole species of the family Cystoviridae
Archives of Virology, 2018Co-Authors: Sari Mäntynen, Lotta-riina Sundberg, Minna M. PoranenAbstract:Cystoviridae is a family of bacterial viruses (bacterioPhages) with a tri-segmented dsRNA genome. It includes a single genus Cystovirus , which has presently only one recognised virus species, Pseudomonas virus phi6 . However, a large number of additional dsRNA Phages have been isolated from various environmental samples, indicating that such viruses are more widespread and abundant than previously recognised. Six of the additional dsRNA Phage isolates (Pseudomonas Phages phi8, phi12, phi13, phi2954, phiNN and phiYY) have been fully sequenced. They all infect Pseudomonas species, primarily plant pathogenic Pseudomonas syringae strains. Due to the notable genetic and structural similarities with Pseudomonas Phage phi6, we propose that these viruses should be included into the Cystovirus genus (and consequently into the Cystoviridae family). Here, we present an updated taxonomy of the family Cystoviridae and give a short overview of the properties of the type member phi6 as well as the putative new members of the family.
