125 results on '"K. A. Bamford"'
Search Results
2. Phage-driven loss of virulence in a fish pathogenic bacterium.
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Elina Laanto, Jaana K H Bamford, Jouni Laakso, and Lotta-Riina Sundberg
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Medicine ,Science - Abstract
Parasites provide a selective pressure during the evolution of their hosts, and mediate a range of effects on ecological communities. Due to their short generation time, host-parasite interactions may also drive the virulence of opportunistic bacteria. This is especially relevant in systems where high densities of hosts and parasites on different trophic levels (e.g. vertebrate hosts, their bacterial pathogens, and virus parasitizing bacteria) co-exist. In farmed salmonid fingerlings, Flavobacterium columnare is an emerging pathogen, and phage that infect F. columnare have been isolated. However, the impact of these phage on their host bacterium is not well understood. To study this, four strains of F. columnare were exposed to three isolates of lytic phage and the development of phage resistance and changes in colony morphology were monitored. Using zebrafish (Danio rerio) as a model system, the ancestral rhizoid morphotypes were associated with a 25-100% mortality rate, whereas phage-resistant rough morphotypes that lost their virulence and gliding motility (which are key characteristics of the ancestral types), did not affect zebrafish survival. Both morphotypes maintained their colony morphologies over ten serial passages in liquid culture, except for the low-virulence strain, Os06, which changed morphology with each passage. To our knowledge, this is the first report of the effects of phage-host interactions in a commercially important fish pathogen where phage resistance directly correlates with a decline in bacterial virulence. These results suggest that phage can cause phenotypic changes in F. columnare outside the fish host, and antagonistic interactions between bacterial pathogens and their parasitic phage can favor low bacterial virulence under natural conditions. Furthermore, these results suggest that phage-based therapies can provide a disease management strategy for columnaris disease in aquaculture.
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- 2012
- Full Text
- View/download PDF
3. High temperature and bacteriophages can indirectly select for bacterial pathogenicity in environmental reservoirs.
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Ville-Petri Friman, Teppo Hiltunen, Matti Jalasvuori, Carita Lindstedt, Elina Laanto, Anni-Maria Örmälä, Jouni Laakso, Johanna Mappes, and Jaana K H Bamford
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Medicine ,Science - Abstract
The coincidental evolution hypothesis predicts that traits connected to bacterial pathogenicity could be indirectly selected outside the host as a correlated response to abiotic environmental conditions or different biotic species interactions. To investigate this, an opportunistic bacterial pathogen, Serratia marcescens, was cultured in the absence and presence of the lytic bacteriophage PPV (Podoviridae) at 25°C and 37°C for four weeks (N = 5). At the end, we measured changes in bacterial phage-resistance and potential virulence traits, and determined the pathogenicity of all bacterial selection lines in the Parasemia plantaginis insect model in vivo. Selection at 37°C increased bacterial motility and pathogenicity but only in the absence of phages. Exposure to phages increased the phage-resistance of bacteria, and this was costly in terms of decreased maximum population size in the absence of phages. However, this small-magnitude growth cost was not greater with bacteria that had evolved in high temperature regime, and no trade-off was found between phage-resistance and growth rate. As a result, phages constrained the evolution of a temperature-mediated increase in bacterial pathogenicity presumably by preferably infecting the highly motile and virulent bacteria. In more general perspective, our results suggest that the traits connected to bacterial pathogenicity could be indirectly selected as a correlated response by abiotic and biotic factors in environmental reservoirs.
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- 2011
- Full Text
- View/download PDF
4. Scoping the effectiveness and evolutionary obstacles in using plasmid-dependent phages to fight antibiotic resistance
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Jaana K. H. Bamford, Teppo Hiltunen, Ville Ojala, Matti Jalasvuori, Sari Mattila, and Ville Hoikkala
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0301 basic medicine ,Microbiology (medical) ,Phage therapy ,medicine.medical_treatment ,030106 microbiology ,Biology ,medicine.disease_cause ,Microbiology ,03 medical and health sciences ,Plasmid ,Antibiotic resistance ,Drug Resistance, Bacterial ,Escherichia coli ,medicine ,Humans ,Bacteriophages ,Escherichia coli Infections ,Genetics ,Bacterial conjugation ,Pathogenic bacteria ,Anti-Bacterial Agents ,Lytic cycle ,Conjugation, Genetic ,Horizontal gene transfer ,Plasmids - Abstract
Aim: To investigate the potential evolutionary obstacles in the sustainable therapeutic use of plasmid-dependent phages to control the clinically important conjugative plasmid-mediated dissemination of antibiotic resistance genes to pathogenic bacteria. Materials & methods: The lytic plasmid-dependent phage PRD1 and the multiresistance conferring plasmid RP4 in an Escherichia coli host were utilized to assess the genetic and phenotypic changes induced by combined phage and antibiotic selection. Results & conclusions: Resistance to PRD1 was always coupled with either completely lost or greatly reduced conjugation ability. Reversion to full conjugation efficiency was found to be rare, and it also restored the susceptibility to plasmid-dependent phages. Consequently, plasmid-dependent phages constitute an interesting candidate for development of sustainable anticonjugation/antiresistance therapeutic applications.
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- 2016
5. High Nutrient Concentration Can Induce Virulence Factor Expression and Cause Higher Virulence in an Environmentally Transmitted Pathogen
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Anssi Lipponen, Reetta Penttinen, Lotta-Riina Sundberg, Hanna Kinnula, and Jaana K. H. Bamford
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0301 basic medicine ,Virulence Factors ,030106 microbiology ,virulence factors ,Soil Science ,Virulence ,Biology ,Real-Time Polymerase Chain Reaction ,Flavobacterium ,Virulence factor ,flavobacterium columnare ,Microbiology ,Fish Diseases ,03 medical and health sciences ,Microbial ecology ,nutrients ,colony type ,Animals ,Collagenases ,Pathogen ,Gene ,Ecology, Evolution, Behavior and Systematics ,Chondroitin Lyases ,Ecology ,Host (biology) ,RT-qPCR ,Environmental Exposure ,chondroitinase ,biology.organism_classification ,collagenase ,030104 developmental biology ,Food ,Oncorhynchus mykiss ,Flavobacterium columnare ,Water Microbiology ,Bacteria - Abstract
Environmentally transmitted opportunistic pathogens shuttle between two substantially different environments: outside-host and within-host habitats. These environments differ from each other especially with respect to nutrient availability. Consequently, the pathogens are required to regulate their behavior in response to environmental cues in order to survive, but how nutrients control the virulence in opportunistic pathogens is still poorly understood. In this study, we examined how nutrient level in the outside-host environment affects the gene expression of putative virulence factors of the opportunistic fish pathogen Flavobacterium columnare. The impact of environmental nutrient concentration on bacterial virulence was explored by cultivating the bacteria in various nutrient conditions, measuring the gene expression of putative virulence factors with RT-qPCR and, finally, experimentally challenging rainbow trout (Oncorhynchus mykiss) fry with these bacteria. Our results show that increased environmental nutrient concentration can increase the expression of putative virulence genes, chondroitinase (cslA) and collagenase, in the outside-host environment and may lead to more rapid fish mortality. These findings address that the environmental nutrients may act as significant triggers of virulence gene expression and therefore contribute to the interaction between an environmentally transmitted opportunistic pathogen and its host. peerReviewed
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- 2016
6. Depositional environment and reservoir characterization of the deep offshore Upper Miocene to Early Pliocene Agbada Formation, Niger delta, Nigeria
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A. Moshood Olayiwola and K. Marion Bamford
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Palynology ,010504 meteorology & atmospheric sciences ,Lithology ,Geochemistry ,Geology ,010502 geochemistry & geophysics ,01 natural sciences ,Sedimentary depositional environment ,Facies ,Reservoir modeling ,Transgressive ,Sedimentology ,Siltstone ,0105 earth and related environmental sciences ,Earth-Surface Processes - Abstract
Recently, continued global demand for energy has necessitated more research for a better understanding of depositional environments and petrophysical parameters of reservoir sands in order to discover more petroleum accumulation. Therefore, the integration of lithological and well log data analyses of ditch-cutting samples from Wells A, B and C from the Niger Delta region are utilized to delineate the Upper Miocene and Early Pliocene Agbada Formation's depositional environments and to determine the quality of the delineated reservoir sands. The detailed well log analysis revealed two major electrofacies namely, shale and sand, while lithofacies analysis identified four facies, which are sandstone, siltstone, claystone and mudstone that were deposited in various depositional environments and sequences. Shale (claystone and mudstone) lithology is characterized by irregular and bell gamma-ray log motifs, which may be deposited in basin plain marine and transgressive marine shelf environments that are associated with transgressive depositional sequences. In contrast, sand (sandstone and siltstone) lithology is typified by funnel and cylindrical gamma-ray log motifs that are deposited in crevasse/prograding delta (sub-unit of fluvial/deltaic environment), and slope/inner fan channel and turbidite environments that are correlated to regressive and aggradation depositional sequences, respectively. Furthermore, sedimentology analysis evidenced twelve, four and seven reservoir sands in wells A, B and C, respectively, while qualitative analysis of well logs reveals eighteen (notated as A to R), four (A to D) and fifteen (A to P) reservoir sands in wells A, B and C, respectively. Moreover, palynological analysis shows alternation of transgressive and regressive sequences in wells A, B and C in this study. The prevalence of mangroves, spores, freshwater swamp and lowland rainforest pollen with rare occurrence of savanna pollen characterized the transgressive sequences, while low percentages of these assemblages with high occurrence of savanna pollen signified the regressive sequences in this study. Alternatively, quantitative analysis showed that volumes of shale (Vsh) are generally low and allow distinction of delineated reservoir sands into clean sand zones (
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- 2019
7. The Minor Capsid Protein VP11 of Thermophilic Bacteriophage P23-77 Facilitates Virus Assembly by Using Lipid-Protein Interactions
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Anni M. Moilanen, Alice Pawlowski, Vesa P. Hytönen, Juha A. E. Määttä, Ilona Rissanen, Jaana K. H. Bamford, and Janne A. Ihalainen
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Models, Molecular ,viruses ,Molecular Sequence Data ,Static Electricity ,Immunology ,Microbiology ,Protein–protein interaction ,Bacteriophage ,chemistry.chemical_compound ,Capsid ,Virology ,Bacteriophages ,Amino Acid Sequence ,Thermus ,Peptide sequence ,Protein secondary structure ,protein-lipid systems ,biology ,Virus Assembly ,Structure and Assembly ,Capsomere ,Virion ,Thermus thermophilus ,Lipid Metabolism ,biology.organism_classification ,Lipids ,Molecular biology ,chemistry ,Insect Science ,thermophilic viruses ,Biophysics ,Capsid Proteins ,DNA ,kapsidi - Abstract
Thermus thermophilus bacteriophage P23-77 is the type member of a new virus family of icosahedral, tailless, inner-membrane-containing double-stranded DNA (dsDNA) viruses infecting thermophilic bacteria and halophilic archaea. The viruses have a unique capsid architecture consisting of two major capsid proteins assembled in various building blocks. We analyzed the function of the minor capsid protein VP11, which is the third known capsid component in bacteriophage P23-77. Our findings show that VP11 is a dynamically elongated dimer with a predominantly α-helical secondary structure and high thermal stability. The high proportion of basic amino acids in the protein enables electrostatic interaction with negatively charged molecules, including nucleic acid and large unilamellar lipid vesicles (LUVs). The plausible biological function of VP11 is elucidated by demonstrating the interactions of VP11 with Thermus -derived LUVs and with the major capsid proteins by means of the dynamic-light-scattering technique. In particular, the major capsid protein VP17 was able to link VP11-complexed LUVs into larger particles, whereas the other P23-77 major capsid protein, VP16, was unable to link VP11-comlexed LUVs. Our results rule out a previously suggested penton function for VP11. Instead, the electrostatic membrane association of VP11 triggers the binding of the major capsid protein VP17, thus facilitating a controlled incorporation of the two different major protein species into the assembling capsid. IMPORTANCE The study of thermophilic viruses with inner membranes provides valuable insights into the mechanisms used for stabilization and assembly of protein-lipid systems at high temperatures. Our results reveal a novel way by which an internal membrane and outer capsid shell are linked in a virus that uses two different major protein species for capsid assembly. We show that a positive protein charge is important in order to form electrostatic interactions with the lipid surface, thereby facilitating the incorporation of other capsid proteins on the membrane surface. This implies an alternative function for basic proteins present in the virions of other lipid-containing thermophilic viruses, whose proposed role in genome packaging is based on their capability to bind DNA. The unique minor capsid protein of bacteriophage P23-77 resembles in its characteristics the scaffolding proteins of tailed phages, though it constitutes a substantial part of the mature virion.
- Published
- 2015
8. Bacteriophage GIL01 gp7 interacts with host LexA repressor to enhance DNA binding and inhibit RecA-mediated auto-cleavage
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Margarita Salas, Matej Butala, Gregor Anderluh, Jaana K. H. Bamford, Vesna Hodnik, Nadine Fornelos, Fonds National de la Recherche Luxembourg, Slovenian Research Agency, Ministerio de Economía y Competitividad (España), European Commission, Centre of Excellence in Biological Interactions (Finland), and Academy of Finland
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Gene Expression Regulation, Viral ,SOS response ,bacteriophages ,Transcription, Genetic ,viruses ,Repressor ,Bacillus Phages ,Biology ,bakteriofagit ,Bacteriophage ,03 medical and health sciences ,SOS Response (Genetics) ,Viral Proteins ,Bacterial Proteins ,Lysogenic cycle ,Genetics ,Promoter Regions, Genetic ,SOS Response, Genetics ,Transcription factor ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,LexA repressor ,Gene regulation, Chromatin and Epigenetics ,Serine Endopeptidases ,ta1182 ,DNA ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,3. Good health ,Cell biology ,Repressor Proteins ,enzymes and coenzymes (carbohydrates) ,Rec A Recombinases ,Lytic cycle ,bacteria ,Repressor lexA ,Protein Binding - Abstract
The SOS response in Eubacteria is a global response to DNA damage and its activation is increasingly associated with the movement of mobile genetic elements. The temperate phage GIL01 is induced into lytic growth using the host's SOS response to genomic stress. LexA, the SOS transcription factor, represses bacteriophage transcription by binding to a set of SOS boxes in the lysogenic promoter P1. However, LexA is unable to efficiently repress GIL01 transcription unless the small phage-encoded protein gp7 is also present. We found that gp7 forms a stable complex with LexA that enhances LexA binding to phage and cellular SOS sites and interferes with RecA-mediated auto-cleavage of LexA, the key step in the initiation of the SOS response. Gp7 did not bind DNA, alone or when complexed with LexA. Our findings suggest that gp7 induces a LexA conformation that favors DNA binding but disfavors LexA auto-cleavage, thereby altering the dynamics of the cellular SOS response. This is the first account of an accessory factor interacting with LexA to regulate transcription., Finnish Centre of Excellence in Biological Interactions [252411]; (cofunded under the Marie Curie Actions of the European Commission) [FP7-COFUND];EMBO[ASTF 286-2013 to N.F.]; Academy of Finland [251106 to J.K.B.]; Slovenian Research Agency [P1-0207 to M.B. and I0-0021 to V.H. and G.A.]; Spanish Ministry of Economy and Competitiveness [BFU2011-23645 to M.S.]. Funding for open access charge: Academy of Finland.
- Published
- 2015
9. Subcellular localization of bacteriophage PRD1 proteins in Escherichia coli
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Teemu O. Ihalainen, Hanna M. Oksanen, Maija Vihinen-Ranta, Jenni Karttunen, Janne A. Ihalainen, Jaana K. H. Bamford, Sari Mäntynen, Heli Lehtivuori, Nikolai V. Tkachenko, and Biophysics Photosynthesis/Energy
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Cancer Research ,Viral protein ,viruses ,Intracellular Space ,Biology ,medicine.disease_cause ,Bacterial cell structure ,Protein–protein interaction ,Viral Proteins ,03 medical and health sciences ,Virology ,Escherichia coli ,medicine ,Bacteriophage PRD1 ,030304 developmental biology ,0303 health sciences ,Bacteria ,030302 biochemistry & molecular biology ,DNA replication ,ta1182 ,Protein interactions ,Fusion protein ,Virus assembly ,Cell biology ,Confocal microscopy ,Protein Transport ,Infectious Diseases ,Membrane protein ,Virion assembly ,Membrane virus - Abstract
Bacteria possess an intricate internal organization resembling that of the eukaryotes. The complexity is especially prominent at the bacterial cell poles, which are also known to be the preferable sites for some bacteriophages to infect. Bacteriophage PRD1 is a well-known model serving as an ideal system to study structures and functions of icosahedral internal membrane-containing viruses. Our aim was to analyze the localization and interactions of individual PRD1 proteins in its native host Escherichia coli. This was accomplished by constructing a vector library for production of fluorescent fusion proteins. Analysis of solubility and multimericity of the fusion proteins, as well as their localization in living cells by confocal microscopy, indicated that multimeric PRD1 proteins were prone to localize in the cell poles. Furthermore, PRD1 spike complex proteins P5 and P31, as fusion proteins, were shown to be functional in the virion assembly. In addition, they were shown to co-localize in the specific polar area of the cells, which might have a role in the multimerization and formation of viral protein complexes.
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- 2014
10. Fluorescence Properties of the Chromophore-Binding Domain of Bacteriophytochrome from Deinococcus radiodurans
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Heikki Takala, Ilona Rissanen, Heli Lehtivuori, Nikolai V. Tkachenko, Janne A. Ihalainen, Jaana K. H. Bamford, and Biophysics Photosynthesis/Energy
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Time Factors ,Fluorescence in the life sciences ,Photochemistry ,chemistry.chemical_compound ,Bimolecular fluorescence complementation ,Bacterial Proteins ,Escherichia coli ,Materials Chemistry ,Physical and Theoretical Chemistry ,ta116 ,Biliverdin ,biology ,Phytochrome ,Biliverdine ,ta1182 ,Deinococcus radiodurans ,Chromophore ,biology.organism_classification ,Fluorescence ,Recombinant Proteins ,Protein Structure, Tertiary ,Surfaces, Coatings and Films ,chemistry ,Mutation ,Quantum Theory ,Spectrophotometry, Ultraviolet ,Deinococcus ,Binding domain - Abstract
Fluorescent proteins are versatile tools for molecular imaging. In this study, we report a detailed analysis of the absorption and fluorescence properties of the chromophore-binding domain from Deinococcus radiodurans and its D207H mutant. Using single photon counting and transient absorption techniques, the average excited state lifetime of both studied systems was about 370 ps. The D207H mutation slightly changed the excited state decay profile but did not have a considerable effect on the average decay time of the system or the shape of the absorption and emission spectra of the biliverdin chromophore. We confirmed that the fluorescence properties of both samples are very similar in vivo and in vitro. However, we found that the paraformaldehyde fixation of the Escherichia coli cells containing the recombinant phytochrome protein significantly changed the fluorescence properties of the chromophore-binding domain. The biliverdin fluorescence was diminished almost completely, and the fluorescence originated only from the protoporphyrin molecules. Our results emphasize that the effect of protoporphyrin IXa should not be ignored in the fluorescence experiments with phytochrome systems while designing better red fluorescence markers for cellular imaging.
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- 2013
11. Identification of five novel tectiviruses in Bacillus strains: analysis of a highly variable region generating genetic diversity
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Jaana K. H. Bamford, Jacques Mahillon, Annika Gillis, Saara Palmu, Hanna Kokko, Nadine Fornelos, and Matti Jalasvuori
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Molecular Sequence Data ,Bacillus ,Bacillus Phages ,Microbiology ,Genome ,Bacteriophage ,Microscopy, Electron, Transmission ,Lysogenic cycle ,Genetic variation ,Amino Acid Sequence ,Genetic variability ,Molecular Biology ,Gene ,Genetics ,Genetic diversity ,biology ,Virion ,ta1182 ,Genetic Variation ,Sequence Analysis, DNA ,General Medicine ,biology.organism_classification ,Bacillus Phage ,DNA, Viral ,Sequence Alignment ,Tectiviridae - Abstract
Our biosphere is abundant with unique and small genes for which no homologs are known. These genes, often referred to as orphans or ORFans, are commonly found in bacteriophage genomes but their origins remain unclear. We discovered five novel tectivirus-like genetic elements by screening more than five-hundred Bacillus strains. A highly variable region (HVR) of these viruses was shown to harbor ORFans in most of these otherwise well-conserved bacteriophages. Previous studies demonstrated that mutations close to this region dramatically alter bacteriophage gene regulation, suggesting that the acquisition of those ORFans may provide a source of genetic diversity that is then subject to genetic selection during bacteriophage evolution. © 2012 Institut Pasteur.
- Published
- 2013
12. Crystallization and preliminary crystallographic analysis of the major capsid proteins VP16 and VP17 of bacteriophage P23-77
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Alice Pawlowski, David I. Stuart, Jonathan M. Grimes, Jaana K. H. Bamford, Karl Harlos, and Ilona Rissanen
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kapsidiproteiinit ,congenital, hereditary, and neonatal diseases and abnormalities ,Lineage (genetic) ,bacteriophages ,crystallization ,Icosahedral symmetry ,viruses ,Biophysics ,Bacteriophage P23-77 ,major coat proteins ,Crystallography, X-Ray ,Biochemistry ,capsid proteins ,bakteriofagit ,law.invention ,Bacteriophage ,03 medical and health sciences ,Structural Biology ,law ,Genetics ,Coat Proteins ,Crystallization ,skin and connective tissue diseases ,double beta-barrel viral lineage ,030304 developmental biology ,0303 health sciences ,biology ,bakteriofaagit ,030306 microbiology ,Thermus thermophilus ,ta1183 ,ta1182 ,biochemical phenomena, metabolism, and nutrition ,Condensed Matter Physics ,biology.organism_classification ,3. Good health ,Crystallography ,Capsid ,Crystallization Communications ,Recombinant DNA ,health occupations ,Capsid Proteins - Abstract
The major capsid proteins VP16 and VP17 of bacteriophage P23-77 have been crystallized using both recombinant and purified virus and preliminary diffraction analyses have been performed., Members of the diverse double-β-barrel lineage of viruses are identified by the conserved structure of their major coat protein. New members of this lineage have been discovered based on structural analysis and we are interested in identifying relatives that utilize unusual versions of the double-β-barrel fold. One candidate for such studies is P23-77, an icosahedral dsDNA bacteriophage that infects the extremophile Thermus thermophilus. P23-77 has two major coat proteins, namely VP16 and VP17, of a size consistent with a single-β-barrel core fold. These previously unstudied proteins have now been successfully expressed as recombinant proteins, purified and crystallized using hanging-drop and sitting-drop vapour-diffusion methods. Crystals of coat proteins VP16 and VP17 have been obtained as well as of a putative complex. In addition, virus-derived material has been crystallized. Diffraction data have been collected to beyond 3 Å resolution for five crystal types and structure determinations are in progress.
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- 2016
13. Membrane structure and interactions with protein and DNA in bacteriophage PRD1
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Nicola G. A. Abrescia, Geoffrey C. Sutton, J.M. Diprose, David I. Stuart, George J. Thomas, Jonathan M. Grimes, Joseph J.B. Cockburn, James M. Benevides, Jaana K. H. Bamford, and Dennis H. Bamford
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viruses ,Lipid Bilayers ,Biology ,Crystallography, X-Ray ,Viral Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Capsid ,Viral envelope ,Cardiolipin ,Bacteriophage PRD1 ,Lipid bilayer ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,Virus Assembly ,Cell Membrane ,030302 biochemistry & molecular biology ,Membrane structure ,Biological membrane ,Viral membrane ,Membrane ,Biochemistry ,chemistry ,DNA, Viral ,Biophysics ,lipids (amino acids, peptides, and proteins) ,Bacterial virus - Abstract
Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated proteins present considerable difficulties for structural analysis. Although enveloped viruses have been imaged at about 9 A resolution by cryo-electron microscopy and image reconstruction1,2, no detailed crystallographic structure of a membrane system has been described. The structure of the bacteriophage PRD1 particle, determined by X-ray crystallography at about 4 A resolution, allows the first detailed analysis of a membrane-containing virus3. The architecture of the viral capsid and its implications for virus assembly are presented in the accompanying paper3. Here we show that the electron density also reveals the icosahedral lipid bilayer, beneath the protein capsid, enveloping the viral DNA. The viral membrane contains about 26,000 lipid molecules asymmetrically distributed between the membrane leaflets. The inner leaflet is composed predominantly of zwitterionic phosphatidylethanolamine molecules, facilitating a very close interaction with the viral DNA, which we estimate to be packaged to a pressure of about 45 atm, factors that are likely to be important during membrane-mediated DNA translocation into the host cell. In contrast, the outer leaflet is enriched in phosphatidylglycerol and cardiolipin, which show a marked lateral segregation within the icosahedral asymmetric unit. In addition, the lipid headgroups show a surprising degree of order.
- Published
- 2016
14. Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid
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Jaana K. H. Bamford, Roger M. Burnett, Dennis H. Bamford, Juha T. Huiskonen, Sarah J. Butcher, Stephen D. Fuller, and Carmen San Martín
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Models, Molecular ,viruses ,Biology ,Crystallography, X-Ray ,Biochemistry ,Genome ,Virus ,03 medical and health sciences ,chemistry.chemical_compound ,Capsid ,Bacteriophage PRD1 ,Structural Biology ,Genetics ,Cloning, Molecular ,030304 developmental biology ,0303 health sciences ,Molecular interactions ,030302 biochemistry & molecular biology ,Capsomere ,Intracellular Membranes ,Crystallography ,Membrane ,chemistry ,Biophysics ,DNA - Abstract
Bacteriophage PRD1 shares many structural and functional similarities with adenovirus. A major difference is the PRD1 internal membrane, which acts in concert with vertex proteins to translocate the phage genome into the host. Multiresolution models of the PRD1 capsid, together with genetic analyses, provide fine details of the molecular interactions associated with particle stability and membrane dynamics. The N- and C-termini of the major coat protein (P3), which are required for capsid assembly, act as conformational switches bridging capsid to membrane and linking P3 trimers. Electrostatic P3-membrane interactions increase virion stability upon DNA packaging. Newly revealed proteins suggest how the metastable vertex works and how the capsid edges are stabilized.
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- 2016
15. Diffraction quality crystals of PRD1, a 66-MDa dsDNA virus with an internal membrane
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Jaana K. H. Bamford, Jonathan M. Grimes, David I. Stuart, Dennis H. Bamford, J.M. Diprose, Geoff Sutton, and Joseph J.B. Cockburn
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Diffraction ,Materials science ,Lipid Bilayers ,Crystallography, X-Ray ,Open Reading Frames ,03 medical and health sciences ,Structural Biology ,Atomic model ,Scattering, Radiation ,Molecule ,Bacteriophage PRD1 ,Bacteriophages ,Lipid bilayer ,Integral membrane protein ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Cell Membrane ,Salmonella enterica ,Lipid Metabolism ,Lipids ,Crystallography ,Membrane ,Membrane protein ,DNA, Viral ,X-ray crystallography ,Electrophoresis, Polyacrylamide Gel - Abstract
It has proved difficult to obtain well diffracting single crystals of macromolecular complexes rich in lipid. We report here the path that has led to crystals of the bacteriophage PRD1, a particle containing approximately 2000 protein subunits from 18 different protein species, around 10 of which are integral membrane proteins associated with a host-derived lipid bilayer of some 12 500 lipid molecules. These crystals are capable of diffracting X-rays to Bragg spacings below 4 A. It is hoped that some lessons learned from PRD1 will be applicable to other lipidic systems and that these crystals will allow, as a proof of principle, the determination of the structure of the virus in terms of a detailed atomic model.
- Published
- 2016
16. Phage Specificity of the Freshwater Fish Pathogen Flavobacterium columnare
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Jaana K. H. Bamford, Elina Laanto, and Lotta-Riina Sundberg
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Phage therapy ,viruses ,medicine.medical_treatment ,Fish farming ,Molecular Sequence Data ,Fresh Water ,Flavobacterium ,Applied Microbiology and Biotechnology ,Host Specificity ,Microbiology ,Fish Diseases ,Flavobacteriaceae Infections ,Environmental Microbiology ,medicine ,Animals ,Bacteriophages ,Pathogen ,Finland ,Ecology ,biology ,Host (biology) ,Fishes ,Sequence Analysis, DNA ,biology.organism_classification ,Virology ,DNA, Viral ,Flavobacterium columnare ,Freshwater fish ,Bacteria ,Food Science ,Biotechnology - Abstract
Flavobacteria and their phages were isolated from Finnish freshwaters and fish farms. Emphasis was placed on finding phages infecting the fish pathogen Flavobacterium columnare for use as phage therapy agents. The host ranges of the flavobacterial phages varied, phages infecting F. columnare being more host specific than the other phages.
- Published
- 2011
17. The use of low-resolution phasing followed by phase extension from 7.6 to 2.5 Å resolution with noncrystallographic symmetry to solve the structure of a bacteriophage capsid protein
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Hanna M. Oksanen, Dennis H. Bamford, David I. Stuart, Jonathan M. Grimes, Jaana K. H. Bamford, and Nicola G. A. Abrescia
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Models, Molecular ,0303 health sciences ,Electron density ,biology ,Low resolution ,030303 biophysics ,General Medicine ,Crystallography, X-Ray ,biology.organism_classification ,Bacteriophage PM2 ,Phaser ,Flattening ,Protein Structure, Tertiary ,Bacteriophage ,03 medical and health sciences ,Crystallography ,Capsid ,Structural Biology ,Bacteriophages ,Capsid Proteins ,Molecular replacement ,Protein Structure, Quaternary ,030304 developmental biology - Abstract
P2, the major capsid protein of bacteriophage PM2, adopts the double β-barrel fold characteristic of the PRD1-adenoviral lineage. The 2.5 Å resolution X-ray data obtained by analysis of the two major lattices of a multiple crystal of P2 were phased by molecular replacement, using as a search model structure factors to 7.6 Å resolution obtained from electron density cut from the map of the entire PM2 virion. Phase extension to 2.5 Å resolution used solely sixfold cycling averaging and solvent flattening. This represents an atypical example of an oligomeric protein for which the structure has been determined at high resolution by bootstrapping from low-resolution initial phases.
- Published
- 2011
18. Bacteriophage selection against a plasmid-encoded sex apparatus leads to the loss of antibiotic-resistance plasmids
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Angus Buckling, Matti Jalasvuori, Anne Nieminen, Jaana K. H. Bamford, and Ville-Petri Friman
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Salmonella typhimurium ,viruses ,R Factors ,medicine.disease_cause ,Polymerase Chain Reaction ,Microbiology ,Bacteriophage ,Plasmid ,Antibiotic resistance ,Kanamycin ,Drug Resistance, Bacterial ,medicine ,Bacteriophage PRD1 ,Selection, Genetic ,Escherichia coli ,Phage typing ,Genetics ,Evolutionary Biology ,biology ,Escherichia coli K12 ,ta1182 ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Anti-Bacterial Agents ,Salmonella enterica ,Conjugation, Genetic ,Genetic Fitness ,General Agricultural and Biological Sciences ,Bacteria ,medicine.drug - Abstract
Antibiotic-resistance genes are often carried by conjugative plasmids, which spread within and between bacterial species. It has long been recognized that some viruses of bacteria (bacteriophage; phage) have evolved to infect and kill plasmid-harbouring cells. This raises a question: can phages cause the loss of plasmid-associated antibiotic resistance by selecting for plasmid-free bacteria, or can bacteria or plasmids evolve resistance to phages in other ways? Here, we show that multiple antibiotic-resistance genes containing plasmids are stably maintained in bothEscherichia coliandSalmonella entericain the absence of phages, while plasmid-dependent phage PRD1 causes a dramatic reduction in the frequency of antibiotic-resistant bacteria. The loss of antibiotic resistance in cells initially harbouring RP4 plasmid was shown to result from evolution of phage resistance where bacterial cells expelled their plasmid (and hence the suitable receptor for phages). Phages also selected for a low frequency of plasmid-containing, phage-resistant bacteria, presumably as a result of modification of the plasmid-encoded receptor. However, these double-resistant mutants had a growth cost compared with phage-resistant but antibiotic-susceptible mutants and were unable to conjugate. These results suggest that bacteriophages could play a significant role in restricting the spread of plasmid-encoded antibiotic resistance.
- Published
- 2011
19. Evolutionary rescue of bacteria via horizontal gene transfer under a lethal β-lactam concentration
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Matti Jalasvuori, Jaana K. H. Bamford, Ville Ojala, Ville Hoikkala, and Sari Mattila
- Subjects
Microbiology (medical) ,Genetics ,biology ,medicine.drug_class ,Immunology ,Antibiotics ,ta1182 ,biology.organism_classification ,Microbiology ,Antibiotic resistance ,Plasmid ,Ampicillin ,Horizontal gene transfer ,medicine ,Immunology and Allergy ,Mobile genetic elements ,Pathogen ,Bacteria ,medicine.drug - Abstract
β-Lactams are a commonly used class of bactericidal antibiotics. The number of β-lactam-resistant pathogens is constantly increasing in hospitals around the world. Interestingly, most of the β-lactam-resistant bacteria carry mobile genetic elements, such as conjugative plasmids, that render the pathogen resistant. These elements mediate their own transfer from one bacterium to another, producing new resistant strains via horizontal gene transfer. Here we investigated whether it is possible that transfer of the resistance element from another bacterium may evolutionarily rescue a susceptible bacterium exposed to a lethal concentration of the β-lactam ampicillin. Indeed, the rescuing occurs even at very high, clinically significant antibiotic levels, suggesting that pathogens may acquire the resistance 'on the fly' from commensal bacteria during treatment.
- Published
- 2014
20. A Unique Group of Virus-Related, Genome-Integrating Elements Found Solely in the Bacterial Family Thermaceae and the Archaeal Family Halobacteriaceae
- Author
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Jaana K. H. Bamford, Matti Jalasvuori, and Alice Pawlowski
- Subjects
Archaeal Viruses ,Genetics ,Halobacteriaceae ,Bacteria ,Genomics and Proteomics ,viruses ,Lineage (evolution) ,Thermus ,Molecular Sequence Data ,Biology ,biology.organism_classification ,Microbiology ,Genome ,Genome, Archaeal ,Phylogenetics ,Bacteriophages ,Halomicrobium ,Molecular Biology ,Gene ,Genome, Bacterial ,Phylogeny ,Meiothermus - Abstract
Viruses SH1 and P23-77, infecting archaeal Haloarcula species and bacterial Thermus species, respectively, were recently designated to form a novel viral lineage. In this study, the lineage is expanded to archaeal Halomicrobium and bacterial Meiothermus species by analysis of five genome-integrated elements that share the core genes with these viruses.
- Published
- 2010
21. Dynamics of a Laterally Evolving Community of Ribozyme-Like Agents as Studied with a Rule-Based Computing System
- Author
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Maija P. Jalasvuori, Matti Jalasvuori, and Jaana K. H. Bamford
- Subjects
Genetics ,Natural selection ,biology ,Origin of Life ,Dynamics (mechanics) ,Ribozyme ,Rule-based system ,General Medicine ,Biological Evolution ,Models, Biological ,Computing systems ,Replication (computing) ,Order (biology) ,Space and Planetary Science ,Evolutionary biology ,biology.protein ,Animals ,Computer Simulation ,RNA, Catalytic ,Evolutionary dynamics ,Software ,Ecology, Evolution, Behavior and Systematics - Abstract
The very early forms of life probably comprised ribozyme-like agents that were able to catalyze reactions and serve as templates for their own replication. The early evolution has also been suggested to occur mainly horizontally between proto-cells or inorganic compartments rather than vertically from parent cell to their dividing siblings. In order to study the evolutionary dynamics of such a community a rule-based computing system entitled as PrimordialEvo was developed. The system simulates a three dimensional matrix of compartments in which replicators, resource collectors and various other actors thrive. Horizontal movement between compartments may be due to genetically induced vesicle formation or random drift. Analysis of the simulation experiments suggests that active sharing of innovations between compartments is important for the overall reproductive success of life. The capability of natural selection to favor genes in the system was also tested, and, for example, the frequency of anti-parasites was observed to increase when parasites were allowed to emerge.
- Published
- 2009
22. On the astrobiological relevance of viruses in extraterrestrial ecosystems
- Author
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Matti Jalasvuori, Anni-Maria Örmälä, and Jaana K. H. Bamford
- Subjects
Physics and Astronomy (miscellaneous) ,Space and Planetary Science ,Ecology ,Panspermia ,Extraterrestrial life ,Earth and Planetary Sciences (miscellaneous) ,Context (language use) ,Ecosystem ,Biology ,Ecology, Evolution, Behavior and Systematics ,Astrobiology - Abstract
Viruses are the dominant form of genetically reproducing entities on Earth. Yet, viruses are mostly neglected in the context of astrobiology due to their non-living nature. In this discussion it is considered whether viruses are likely to be transferred within bacterial endospores to other planetary bodies through lithopanspermia. Interestingly, it seems possible that ecosystems of panspermial origin might yield biospheres in which viruses are absent. The evolutionary pathway of life in these systems might differ significantly from the path observed on Earth. We hypothesize that the difference in the two potential ways for the emergence of life, those being panspermial or local origin, on any certain planet could be clarified by analyzing the diversity of virosphere on the planet. The use of viruses as putative biomarkers is also discussed and studied.
- Published
- 2009
23. Purified Membrane-Containing Procapsids of Bacteriophage PRD1 Package the Viral Genome
- Author
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Jaana K. H. Bamford, Gabija Ziedaite, Dennis H. Bamford, and Hanna M. Kivelä
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Viral Plaque Assay ,viruses ,ATPase ,Genome ,Viral Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Capsid ,Bacteriophage PRD1 ,Structural Biology ,Molecular Biology ,Integral membrane protein ,030304 developmental biology ,0303 health sciences ,Microbial Viability ,biology ,030306 microbiology ,Virus Assembly ,Cell Membrane ,Membrane Proteins ,Molecular biology ,Membrane ,chemistry ,DNA, Viral ,biology.protein ,Biophysics ,Tectiviridae ,DNA - Abstract
Icosahedral-tailed double-stranded DNA (dsDNA) bacteriophages and herpesviruses translocate viral DNA into a preformed procapsid in an ATP-driven reaction by a packaging complex that operates at a portal vertex. A similar packaging system operates in the tailless dsDNA phage PRD1 (Tectiviridae family), except that there is an internal membrane vesicle in the procapsid. The unit-length linear dsDNA genome with covalently linked 5'-terminal proteins enters the procapsid through a unique vertex. Two small integral membrane proteins, P20 and P22, provide a conduit for DNA translocation. The packaging machinery also contains the packaging ATPase P9 and the packaging efficiency factor P6. Here we describe a method used to obtain purified packaging-competent PRD1 procapsids. The optimized in vitro packaging system allowed efficient packaging of defined DNA substrates. We determined that the genome terminal protein P8 is necessary for packaging and provided an estimation of the packaging rate.
- Published
- 2009
24. Structural Co-Evolution of Viruses and Cells in the Primordial World
- Author
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Matti Jalasvuori and Jaana K. H. Bamford
- Subjects
Bacteria ,viruses ,General Medicine ,Biological evolution ,Virus Physiological Phenomena ,Biology ,Bacterial Physiological Phenomena ,Biological Evolution ,Virology ,Cellular life ,RNA world hypothesis ,Cell Wall ,Space and Planetary Science ,Evolutionary biology ,Viral evolution ,Host-Pathogen Interactions ,Viruses ,Ecology, Evolution, Behavior and Systematics - Abstract
Viruses and cells co-evolve due to the parasitic nature of viruses. Yet there are no models suggesting how the unicellular organisms and their viruses might co-evolve structurally. Here, in this study, we plunge into this unexplored field from a wide perspective and try to describe some of the intriguing ways in which viruses may have shaped the cellular life forms on the ancient Earth. At first we propose a scenario where viruses act as a driving force in the emergence of bacterial cell walls by providing favorable intermediates for the otherwise improbable steps in the cell wall generation. We also discuss the role of viruses in the evolution of cell surface components such as receptors and second membranes. Finally we focus on hypothetical proto-viruses, the selfish abusers of the RNA-world, in explaining some of the very early stages in the origin and evolution of life. Proto-viruses may be responsible for creating the first true cells in order to support their selfish needs. In this model we also suggest a logical pathway to explaining the emergence of modern viruses.
- Published
- 2008
25. Studies on ‘usual’ and ‘atypical’ serum cholinesterase using α-naphthyl acetate as substrate
- Author
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K. F. Bamford and H. Harris
- Subjects
chemistry.chemical_classification ,biology ,Serum cholinesterase ,Dibucaine ,Substrate (chemistry) ,Structural difference ,chemistry.chemical_compound ,Enzyme ,chemistry ,Biochemistry ,Naphthyl acetate ,Genetics ,medicine ,biology.protein ,Fluoride ,Genetics (clinical) ,medicine.drug ,Cholinesterase - Abstract
Summary Estimates of the Michaelis constants for usual5 and ‘atypical’ serum cholinesterase with α-naphthyl acetate as substrate were obtained. Expressed as m-moles α-naphthyl acetate per litre the values were: ‘usual’ enzyme 0-76 + 0-056, ‘atypical’ enzyme 0-58 + 0-057. The inhibition of the activity of the two enzymes by dibucaine, RO 2-0683, and fluoride was also examined using α-naphthyl acetate as substrate. It was found that, in the appropriate concentration range, the ‘usual’ enzyme was inhibited to a much greater degree than the ‘atypical’ enzyme by dibucaine and RO 2-0683. With fluoride, however, the difference, though significant, was much less marked. The findings are compared with similar data obtained when choline esters were used as substrates for the enzymes, and are considered in terms of the hypothesis that a structural difference at the ‘anionic’ site is the cause of the difference in the properties of the two enzymes.
- Published
- 2007
26. Efficient DNA Packaging of Bacteriophage PRD1 Requires the Unique Vertex Protein P6
- Author
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Nelli J. Karhu, Gabija Ziedaite, Jaana K. H. Bamford, and Dennis H. Bamford
- Subjects
Specificity factor ,Immunology ,Mutant ,Biology ,medicine.disease_cause ,Microbiology ,Bacteriophage ,Viral Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Virology ,DNA Packaging ,medicine ,Bacteriophage PRD1 ,Lipid bilayer ,030304 developmental biology ,0303 health sciences ,Mutation ,Structure and Assembly ,Virus Assembly ,030302 biochemistry & molecular biology ,Virion ,Tectivirus ,Salmonella enterica ,biology.organism_classification ,Molecular biology ,chemistry ,Capsid ,Insect Science ,Biophysics ,DNA - Abstract
The assembly of bacteriophage PRD1 proceeds via formation of empty procapsids containing an internal lipid membrane, into which the linear double-stranded DNA genome is subsequently packaged. The packaging ATPase P9 and other putative packaging proteins have been shown to be located at a unique vertex of the PRD1 capsid. Here, we describe the isolation and characterization of a suppressor-sensitive PRD1 mutant deficient in the unique vertex protein P6. Protein P6 was found to be an essential part of the PRD1 packaging machinery; its absence leads to greatly reduced packaging efficiency. Lack of P6 was not found to affect particle assembly, because in the P6-deficient mutant infection, wild-type (wt) amounts of particles were produced, although most were empty. P6 was determined not to be a specificity factor, as the few filled particles seen in the P6-deficient infection contained only PRD1-specific DNA. The presence of P6 was not necessary for retention of DNA in the capsid once packaging had occurred, and P6-deficient DNA-containing particles were found to be stable and infectious, albeit not as infectious as wt PRD1 virions. A packaging model for bacteriophage PRD1, based on previous results and those obtained in this study, is presented.
- Published
- 2007
27. Genome Characterization of Lipid-Containing Marine Bacteriophage PM2 by Transposon Insertion Mutagenesis
- Author
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Mart Krupovic, Jaana K. H. Bamford, Dennis H. Bamford, Juha-Matti Aalto, Harri Savilahti, Heikki Vilen, and Hanna M. Kivelä
- Subjects
Transposable element ,Genome evolution ,Molecular Sequence Data ,Immunology ,Mutagenesis (molecular biology technique) ,Genome, Viral ,Biology ,Corticovirus ,complex mixtures ,Microbiology ,Genome ,Evolution, Molecular ,Bacteriophage ,Open Reading Frames ,03 medical and health sciences ,chemistry.chemical_compound ,Virology ,Amino Acid Sequence ,Gene ,030304 developmental biology ,Genetics ,0303 health sciences ,030306 microbiology ,Corticoviridae ,DNA ,Lipid Metabolism ,biology.organism_classification ,Lipids ,Pseudoalteromonas ,Phenotype ,Genetic Diversity and Evolution ,chemistry ,Mutagenesis ,Insect Science ,DNA Transposable Elements - Abstract
Bacteriophage PM2 presently is the only member of the Corticoviridae family. The virion consists of a protein-rich lipid vesicle, which is surrounded by an icosahedral protein capsid. The lipid vesicle encloses a supercoiled circular double-stranded DNA genome of 10,079 bp. PM2 belongs to the marine phage community and is known to infect two gram-negative Pseudoalteromonas species. In this study, we present a characterization of the PM2 genome made using the in vitro transposon insertion mutagenesis approach. Analysis of 101 insertion mutants yielded information on the essential and dispensable regions of the PM2 genome and led to the identification of several new genes. A number of lysis-deficient mutants as well as mutants displaying delayed- and/or incomplete-lysis phenotypes were identified. This enabled us to identify novel lysis-associated genes with no resemblance to those previously described from other bacteriophage systems. Nonessential genome regions are discussed in the context of PM2 genome evolution.
- Published
- 2006
28. The Entry Mechanism of Membrane-Containing Phage Bam35 Infecting Bacillus thuringiensis
- Author
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Rimantas Daugelavičius, Jaana K. H. Bamford, Ausra Gaidelyte, Virginija Cvirkaite-Krupovic, and Dennis H. Bamford
- Subjects
Bacteriophages, Transposons, and Plasmids ,Bacillus thuringiensis ,Bacillus Phages ,Biology ,Microbiology ,Bacteriophage ,Cell membrane ,03 medical and health sciences ,chemistry.chemical_compound ,Endopeptidases ,medicine ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Cell Membrane ,Viral membrane ,biology.organism_classification ,Bacillus Phage ,medicine.anatomical_structure ,chemistry ,Lytic cycle ,Muramic Acids ,Receptors, Virus ,Peptidoglycan ,DNA - Abstract
The temperate double-stranded DNA bacteriophage Bam35 infects gram-positive Bacillus thuringiensis cells. Bam35 has an icosahedral protein coat surrounding the viral membrane that encloses the linear 15-kbp DNA genome. The protein coat of Bam35 uses the same assembly principle as that of PRD1, a lytic bacteriophage infecting gram-negative hosts. In this study, we dissected the process of Bam35 entry into discrete steps: receptor binding, peptidoglycan penetration, and interaction with the plasma membrane (PM). Bam35 very rapidly adsorbs to the cell surface, and N -acetyl-muramic acid is essential for Bam35 binding. Zymogram analysis demonstrated that peptidoglycan-hydrolyzing activity is associated with the Bam35 virion. We showed that the penetration of Bam35 through the PM is a divalent-cation-dependent process, whereas adsorption and peptidoglycan digestion are not.
- Published
- 2006
29. In vitro DNA Packaging of PRD1: A Common Mechanism for Internal-membrane Viruses
- Author
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Jaana K. H. Bamford, Dennis H. Bamford, and Nelli J. Strömsten
- Subjects
viruses ,ATPase ,Molecular Sequence Data ,Cell ,Mutant ,Biology ,Genome ,Virus ,Viral Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Capsid ,Bacterial Proteins ,Structural Biology ,DNA Packaging ,medicine ,Bacteriophage PRD1 ,Amino Acid Sequence ,Molecular Biology ,030304 developmental biology ,Adenosine Triphosphatases ,0303 health sciences ,030306 microbiology ,Genetic Complementation Test ,Molecular biology ,Cell biology ,medicine.anatomical_structure ,chemistry ,Mutagenesis ,DNA, Viral ,biology.protein ,Tectiviridae ,Sequence Alignment ,DNA - Abstract
PRD1 is the type virus of the Tectiviridae family. Its linear double-stranded DNA genome has covalently attached terminal proteins and is surrounded by a membrane, which is further enclosed within an icosahedral protein capsid. Similar to tailed bacteriophages, PRD1 packages its DNA into a preformed procapsid. The PRD1 putative packaging ATPase P9 is a structural protein located at a unique vertex of the capsid. An in vitro system for packaging DNA into preformed empty procapsids was developed. The system uses cell extracts of overexpressed P9 protein and empty procapsids from a P9-deficient mutant virus infection and PRD1 DNA containing a LacZalpha-insert. The in vitro packaged virions produce distinctly blue plaques when plated on a suitable host. This is the first time that a viral genome is packaged in vitro into a membrane vesicle. Comparison of PRD1 P9 with putative packaging ATPase sequences from bacterial, archaeal and eukaryotic viruses revealed a new packaging ATPase-specific motif. Surprisingly the viruses having this packaging ATPase motif, and thus considered to be related, were the same as those recently grouped together using the coat protein fold and virion architecture. Our finding here strongly supports the idea that all these viruses infecting hosts in all domains of life had a common ancestor.
- Published
- 2005
30. Does Common Architecture Reveal a Viral Lineage Spanning All Three Domains of Life?
- Author
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Stacy D. Benson, Roger M. Burnett, Jaana K. H. Bamford, and Dennis H. Bamford
- Subjects
Models, Molecular ,Protein Conformation ,viruses ,Lineage (evolution) ,Molecular Sequence Data ,Biology ,Protein Structure, Secondary ,Adenoviridae ,03 medical and health sciences ,Open Reading Frames ,Protein structure ,Capsid ,Three-domain system ,Animals ,Humans ,Bacteriophage PRD1 ,Cell Lineage ,Amino Acid Sequence ,Non-cellular life ,Peptide sequence ,Molecular Biology ,Virus classification ,030304 developmental biology ,Genetics ,0303 health sciences ,Bacteria ,Sequence Homology, Amino Acid ,030306 microbiology ,Cell Biology ,biology.organism_classification ,Archaea ,Biological Evolution ,Viruses - Abstract
Our discovery that the major coat protein of bacteriophage PRD1 resembles that of human adenovirus raised the unexpected possibility that viruses infecting bacteria could be related by evolution to those infecting animal hosts. We first review the development of this idea. We then describe how we have used structure-based modeling to show that several other viruses with no detectable sequence similarity are likely to have coats constructed from similar proteins-the "double-barrel trimer." There is evidence that the group includes a diversity of viruses infecting very different hosts in all three domains of life: Eukarya; Bacteria; and Archaea that diverged billions of years ago. The current classification of viruses obscures such similarities. We propose that the occurrence of a double-barrel trimer coat protein in an icosahedral dsDNA virus with large facets, irrespective of its host, is a very strong indicator of its membership in a lineage of viruses with a common ancestor.
- Published
- 2004
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31. The Tailless Icosahedral Membrane Virus PRD1 Localizes the Proteins Involved in Genome Packaging and Injection at a Unique Vertex
- Author
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Jaana K. H. Bamford, Dennis H. Bamford, Brent E. Gowen, and Stephen D. Fuller
- Subjects
Immunology ,Genome, Viral ,Microbiology ,Virus ,Single-stranded binding protein ,Viral Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Immunolabeling ,Capsid ,Virology ,Bacteriophage PRD1 ,030304 developmental biology ,0303 health sciences ,biology ,Structure and Assembly ,Virus Assembly ,Cryoelectron Microscopy ,030302 biochemistry & molecular biology ,Virion ,Membrane Proteins ,Intracellular Membranes ,Viral membrane ,Molecular biology ,3. Good health ,Vertex (geometry) ,Cell biology ,Membrane protein ,chemistry ,Insect Science ,biology.protein ,DNA - Abstract
The double-stranded DNA (dsDNA) virus PRD1 carries its genome in a membrane surrounded by an icosahedral protein shell. The shell contains 240 copies of the trimeric P3 protein arranged with a pseudo T = 25 triangulation that is reminiscent of the mammalian adenovirus. DNA packaging and infection are believed to occur through the vertices of the particle. We have used immunolabeling to define the distribution of proteins on the virion surface. Antibodies to protein P3 labeled the entire surface of the virus. Most of the 12 vertices labeled with antibodies directed against proteins P5, P2, and P31. These proteins are known to function in virus binding to the cell surface. Proteins P6, P11, and P20 were found on a single vertex per virion. The P6 and P20 proteins are believed to function in DNA packaging. Protein P11 is a pilot protein that is involved in a complex that mediates the early stages of DNA entry to the host cell. Labeling with antibodies to P5 or P2 did not affect the labeling of P6, the unique vertex protein. Labeling with antibodies to the unique vertex protein P6 interfered with the labeling by antibodies to the unique vertex protein P20. We conclude that PRD1 utilizes 11 of its vertices for initial receptor binding. It utilizes a single, unique vertex for both DNA packing during assembly and DNA delivery during infection.
- Published
- 2003
32. Probing the ability of the coat and vertex protein of the membrane-containing bacteriophage PRD1 to display a meningococcal epitope
- Author
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Jaana K. H. Bamford, Dennis H. Bamford, Liisa Laakkonen, Juha T. Huiskonen, Matti Sarvas, and Maija Toropainen
- Subjects
Vesicle-associated membrane protein 8 ,Phage display ,Capsid protein ,Recombinant Fusion Proteins ,Protein subunit ,Genetic Vectors ,Porins ,Neisseria meningitidis, Serogroup B ,Biology ,Virus Replication ,Epitope ,Virus ,PRD1 ,Epitopes ,03 medical and health sciences ,Capsid ,Virology ,Escherichia coli ,Bacteriophage PRD1 ,Amino Acid Sequence ,Meningococcal epitope ,030304 developmental biology ,Vaccines, Synthetic ,0303 health sciences ,030302 biochemistry & molecular biology ,Molecular biology ,Protein tertiary structure ,3. Good health ,Cell biology ,Mutagenesis, Insertional ,Capsid Proteins ,Vertex protein ,Bacterial outer membrane - Abstract
Bacteriophage PRD1 is an icosahedral dsDNA virus with a diameter of 740 Å and an outer protein shell composed of 720 copies of major coat protein P3. Spike complexes at the vertices are composed of a pentameric base (protein P31) and a spike structure (proteins P5 and P2) where the N-terminal region of the trimeric P5 is associated with the base and the C-terminal region of P5 is associated with receptor-binding protein P2. The functionality of proteins P3 and P5 was investigated using insertions and deletions. It was observed that P3 did not tolerate changes whereas P5 tolerated changes much more freely. These properties support the hypothesis that viruses have core structures and functions, which remain stable over time, as well as other elements, responsible for host interactions, which are evolutionally more fluid. The insertional probe used was the apex of exposed loop 4 of group B meningococcal outer membrane protein PorA, a medically important subunit vaccine candidate. It was demonstrated that the epitope could be displayed on the virus surface as part of spike protein P5.
- Published
- 2003
33. Grain yield and N benefits to sequential wheat and barley crops from single-year alfalfa, berseem and red clover, chickling vetch and lentil
- Author
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S. R. Smith, W. J. Bullied, Martin H. Entz, and K. C. Bamford
- Subjects
food.ingredient ,Plant Science ,Horticulture ,Biology ,biology.organism_classification ,Red Clover ,Crop ,food ,Agronomy ,Lathyrus ,Hay ,Hordeum vulgare ,Trifolium alexandrinum ,Medicago sativa ,Canola ,Agronomy and Crop Science - Abstract
Single-year hay alfalfas (Medicago sativa L.), berseem (Trifolium alexandrinum L.) and red clovers (Trifolium pratense L.), chickling vetch (Lathyrus sativus L.) and lentil (Lens culinaris Medik.) were evaluated for rotational yield and N benefits to the following first-year wheat (Triticum aestivum L.) and second-year barley (Hordeum vulgare L.) crops. Field experiments were initiated in 1997 and 1998 on a Riverdale silty clay soil at Winnipeg, Manitoba. Yield and N content of the following wheat crop were increased following legumes compared to wheat following a canola control. Wheat yield and N content averaged 2955 kg ha–1 and 76.1 kg ha–1, respectively, following the chickling vetch and lentil, 2456 kg ha–1 and 56.4 kg ha–1 following single-year hay legumes, compared with 1706 kg ha–1 and 37.9 kg ha–1 following canola. Non-dormant alfalfas (dormancy rating of eight or greater) contributed to larger grain yields than the dormant alfalfas only in the first year of each experiment. The chickling vetch and lentil provided similar or higher subsequent crop yields and N content for 2 yr compared to a canola control or fallow treatment. This study shows that some increase in yield can be achieved by using a single-year alfalfa hay crop instead of fallow; however, exclusive green manuring of chickling vetch and lentil crops can produce the most increase in yield and N uptake in subsequent crops. Key words: Alfalfa (single-year), legumes (annual), green manure, nitrogen, cropping system
- Published
- 2002
34. Probing protein interactions in the membrane-containing virus PRD1
- Author
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Hanna M. Oksanen, Jaana K. H. Bamford, and Sari Mattila
- Subjects
Viral Structural Proteins ,0303 health sciences ,Vesicle-associated membrane protein 8 ,Macromolecular Substances ,030302 biochemistry & molecular biology ,Mutant ,Membrane Proteins ,Biology ,Virology ,Transmembrane protein ,Protein–protein interaction ,03 medical and health sciences ,Lytic cycle ,Protein Interaction Mapping ,Inner membrane ,Tectiviridae ,Bacteriophage PRD1 ,Electrophoresis, Polyacrylamide Gel ,Protein Multimerization ,Integral membrane protein ,030304 developmental biology - Abstract
PRD1 is a Gram-negative bacteria infecting complex tailless icosahedral virus with an inner membrane. This type virus of the family Tectiviridae contains at least 18 structural protein species, of which several are membrane associated. Vertices of the PRD1 virion consist of complexes recognizing the host cell, except for one special vertex through which the genome is packaged. Despite extensive knowledge of the overall structure of the PRD1 virion and several individual proteins at the atomic level, the locations and interactions of various integral membrane proteins and membrane-associated proteins still remain a mystery. Here, we demonstrated that blue native PAGE can be used to probe protein–protein interactions in complex membrane-containing viruses. Using this technique and PRD1 as a model, we identified the known PRD1 multiprotein vertex structure composed of penton protein P31, spike protein P5, receptor-binding protein P2 and stabilizing protein P16 linking the vertex to the internal membrane. Our results also indicated that two transmembrane proteins, P7 and P14, involved in viral nucleic acid delivery, make a complex. In addition, we performed a zymogram analysis using mutant particles devoid of the special vertex that indicated that the lytic enzyme P15 of PRD1 was not part of the packaging vertex, thus contradicting previously published results.
- Published
- 2014
35. Non-structural proteins P17 and P33 are involved in the assembly of the internal membrane-containing virus PRD1
- Author
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Teemu O. Ihalainen, Sari Mäntynen, Hanna M. Oksanen, Jaana K. H. Bamford, and Jenni Karttunen
- Subjects
assembly ,chaperonin ,viruses ,Mutant ,fluorescence recovery after photobleaching ,Viral Nonstructural Proteins ,medicine.disease_cause ,Virus Replication ,Chaperonin ,Host-Parasite Interactions ,Bacteriophage ,bacteriophage ,Virology ,medicine ,Escherichia coli ,fluorescent protein ,Bacteriophage PRD1 ,membrane virus ,Microscopy, Confocal ,biology ,protein localisation ,Virus Assembly ,ta1182 ,Fluorescence recovery after photobleaching ,GroES ,Chaperonin 60 ,biology.organism_classification ,Fusion protein ,GroEL ,3. Good health ,Cell biology - Abstract
Bacteriophage PRD1, which has been studied intensively at the structural and functional levels, still has some gene products with unknown functions and certain aspects of the PRD1 assembly process have remained unsolved. In this study, we demonstrate that the phage-encoded non-structural proteins P17 and P33, either individually or together, complement the defect in a temperature-sensitive GroES mutant of Escherichia coli for host growth and PRD1 propagation. Confocal microscopy of fluorescent fusion proteins revealed co-localisation between P33 and P17 as well as between P33 and the host chaperonin GroEL. A fluorescence recovery after photobleaching assay demonstrated that the diffusion of the P33 fluorescent fusion protein was substantially slower in E. coli than theoretically calculated, presumably resulting from intermolecular interactions. Our results indicate that P33 and P17 function in procapsid assembly, possibly in association with the host chaperonin complex GroEL/GroES.
- Published
- 2014
36. New enveloped dsRNA phage from freshwater habitat
- Author
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Sari Mäntynen, Janne J. Ravantti, Elina Laanto, Annika Kohvakka, Minna M. Poranen, and Jaana K. H. Bamford
- Subjects
Cystoviridae ,viruses ,Molecular Sequence Data ,Fresh Water ,freshwater habitats ,Genome ,Virus ,Bacteriophage ,03 medical and health sciences ,Virology ,Pseudomonas ,Sequence Homology, Nucleic Acid ,Cluster Analysis ,Bacteriophages ,Finland ,Phylogeny ,030304 developmental biology ,Genetics ,0303 health sciences ,biology ,030306 microbiology ,ta1183 ,ta1182 ,Bacteriophage phi 6 ,Nucleic acid sequence ,Sequence Analysis, DNA ,biology.organism_classification ,RNA silencing ,Lakes ,Molecular virology ,RNA, Viral ,Recombination - Abstract
Cystoviridae is a family of bacteriophages with a tri-segmented dsRNA genome enclosed in a tri-layered virion structure. Here, we present a new putative member of the Cystoviridae family, bacteriophage ϕNN. ϕNN was isolated from a Finnish lake in contrast to the previously identified cystoviruses, which originate from various legume samples collected in the USA. The nucleotide sequence of the virus reveals a strong genetic similarity (~80 % for the L-segments, ~55 % for the M-segments and ~84 % for the S-segments) to Pseudomonas phage ϕ6, the type member of the virus family. However, the relationship between ϕNN and other cystoviruses is more distant. In general, proteins located in the internal parts of the virion were more conserved than those exposed on the virion surface, a phenomenon previously reported among eukaryotic dsRNA viruses. Structural models of several putative ϕNN proteins propose that cystoviral structures are highly conserved.
- Published
- 2014
37. Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae
- Author
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Alice Pawlowski, Matti Jalasvuori, Ilona Rissanen, Mart Krupovic, Jaana K. H. Bamford, University of Jyväskylä (JYU), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), This work was supported by the Finnish Center of Excellence (CoE) program of the Acadamy of Finland 2012-2017 (CoE in Biological Interactions, #252411) and Acadamy of Finland personal grant to MJ (#251O13) and JKHB (#251106)., and Institut Pasteur [Paris]
- Subjects
MESH: Sequence Analysis, DNA ,Genes, Viral ,Prophages ,viruses ,[SDV]Life Sciences [q-bio] ,Molecular Sequence Data ,Sequence Homology ,MESH: Thermus thermophilus ,Bacterial genome size ,dsDNA Virus ,Bacteriophage ,MESH: Prophages ,Virology ,Cluster Analysis ,Bacteriophages ,MESH: Bacteriophages ,MESH: Sequence Homology ,Meiothermus ,MESH: Genes, Viral ,MESH: Molecular Sequence Data ,biology ,Thermus thermophilus ,Thermus ,Capsomere ,DNA Viruses ,Virion ,Sequence Analysis, DNA ,General Medicine ,Gene Synteny ,biology.organism_classification ,Archaea ,Capsid Protein ,MESH: Cluster Analysis ,MESH: DNA Viruses ,3. Good health ,MESH: DNA, Viral ,Temperateness ,tRNA Gene ,Major Capsid Protein ,Capsid ,MESH: Archaea ,DNA, Viral ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,MESH: Virion - Abstract
International audience; A new family of viruses named Sphaerolipoviridae has been proposed recently. It comprises icosahedral, tailless haloarchaeal viruses with an internal lipid membrane located between the protein capsid and the dsDNA genome. The proposed family Sphaerolipoviridae was divided into two genera: Alphasphaerolipovirus, including Haloarcula hispanica viruses SH1, PH1 and HHIV-2, and Betasphaerolipovirus, including Natrinema virus SNJ1. Here, we propose to expand the family Sphaerolipoviridae to include a group of bacteriophages infecting extreme thermophilic Thermus thermophilus and sharing a number of structural and genomic properties with archaeal sphaerolipoviruses. This new group comprises two members, lytic phage P23-77 and temperate phage IN93, as well as putative members P23-72 and P23-65H. In addition, several related proviruses have been discovered as integrated elements in bacterial genomes of the families Thermus and Meiothermus. Morphology of the virus particles and the overall capsid architecture of these bacteriophages resembles that of archaeal members of the Sphaerolipoviridae, including an unusual capsid arrangement in a T = 28 dextro lattice. Alpha- and betasphaerolipoviruses share with P23-77-like bacteriophages a conserved block of core genes that encode a putative genome-packaging ATPase and the two major capsid proteins (MCPs). The recently determined X-ray structure of the small and large MCPs of P23-77 revealed a single beta-barrel (jelly-roll) fold that is superimposable with the cryo-EM density maps of the SH1 capsomers. Given the common features of these viruses, we propose to include the so far unclassified P23-77-like bacteriophages into a new genus, "Gammasphaerolipovirus", within the family Sphaerolipoviridae.
- Published
- 2014
38. The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 Å resolution
- Author
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Stacy D. Benson, Jaana K. H. Bamford, Roger M. Burnett, and Dennis H. Bamford
- Subjects
Models, Molecular ,0303 health sciences ,Molecular Structure ,Chemistry ,Viral protein ,Protein subunit ,030302 biochemistry & molecular biology ,Resolution (electron density) ,Virion ,Trimer ,General Medicine ,Crystal structure ,Crystallography, X-Ray ,medicine.disease_cause ,Lipids ,03 medical and health sciences ,Crystallography ,Capsid ,Solvation shell ,Structural Biology ,Icosahedral viral capsid ,medicine ,Bacteriophage PRD1 ,030304 developmental biology - Abstract
P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now been extended to 1.65 A resolution (R(work) = 19.0% and R(free) = 20.8%). The new high-resolution model shows that P3 forms crystals through hydrophobic patches solvated by 2-methyl-2,4-pentanediol molecules. It reveals details of how the molecule's high stability may be achieved through ordered solvent in addition to intra- and intersubunit interactions. Of particular importance is a 'puddle' at the top of the molecule containing a four-layer deep hydration shell that cross-links a complex structural feature formed by 'trimerization loops'. These loops also link subunits by extending over a neighbor to reach the third subunit in the trimer. As each subunit has two eight-stranded viral jelly rolls, the trimer has a pseudo-hexagonal shape to allow close packing in its 240 hexavalent capsid positions. Flexible regions in P3 facilitate these interactions within the capsid and with the underlying membrane. A selenometh-ionine P3 derivative, with which the structure was solved, has been refined to 2.2 A resolution (R(work) = 20.1% and R(free) = 22.8%). The derivatized molecule is essentially unchanged, although synchrotron radiation has the curious effect of causing it to rotate about its threefold axis. P3 is a second example of a trimeric 'double-barrel' protein that forms a stable building block with optimal shape for constructing a large icosahedral viral capsid. A major difference is that hexon has long variable loops that distinguish different adenovirus species. The short loops in P3 and the severe constraints of its various interactions explain why the PRD1 family has highly conserved coat proteins.
- Published
- 2001
39. A New Mutant Class, Made by Targeted Mutagenesis, of Phage PRD1 Reveals That Protein P5 Connects the Receptor Binding Protein to the Vertex
- Author
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Jaana K. H. Bamford and Dennis H. Bamford
- Subjects
Salmonella typhimurium ,Immunology ,Mutant ,Cloning vector ,Mutagenesis (molecular biology technique) ,Computational biology ,Biology ,medicine.disease_cause ,Microbiology ,Viral Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Capsid ,Plasmid ,Virology ,Escherichia coli ,medicine ,Gene ,030304 developmental biology ,0303 health sciences ,Mutation ,030306 microbiology ,Structure and Assembly ,Virus Assembly ,Molecular biology ,3. Good health ,Microscopy, Electron ,chemistry ,Insect Science ,Mutagenesis, Site-Directed ,Receptors, Virus ,Capsid Proteins ,Electrophoresis, Polyacrylamide Gel ,Adsorption ,DNA ,Tectiviridae - Abstract
Phage PRD1 and adenovirus share a number of structural and functional similarities, one of which is the vertex organization at the fivefold-symmetry positions. We developed an in vitro mutagenesis system for the linear PRD1 genome in order to make targeted mutations. The role of protein P5 in the vertex structure was examined by this method. Mutation in gene V revealed that protein P5 is essential. The absence of P5 did not compromise the particle assembly or DNA packaging but led to a deficient vertex structure where the receptor binding protein P2, in addition to protein P5, was missing. P5 − particles also lost their DNA upon purification. Based on this and previously published information we propose a spatial model for the spike structure at the vertices. This resembles to the corresponding structure in adenovirus.
- Published
- 2000
40. Assembly Dynamics of the Nucleocapsid Shell Subunit (P8) of Bacteriophage φ6
- Author
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Roman Tuma, Dennis H. Bamford, George J. Thomas, and Jaana K. H. Bamford
- Subjects
biology ,Protein Conformation ,Icosahedral symmetry ,Chemistry ,Circular Dichroism ,viruses ,Protein subunit ,Shell (structure) ,RNA polymerase complex ,Deuterium ,Spectrum Analysis, Raman ,biology.organism_classification ,Biochemistry ,Virology ,Protein Structure, Secondary ,Bacteriophage phi 6 ,Bacteriophage ,RNA silencing ,Solubility ,Viral envelope ,Pseudomonas syringae ,Nucleocapsid ,Hydrogen - Abstract
Phi6 is an enveloped dsRNA bacteriophage of Pseudomonas syringae. The viral envelope encloses a nucleocapsid, consisting of an RNA-dependent RNA polymerase complex within an icosahedral shell assembled from approximately 800 copies of a 16 kDa subunit (protein P8, encoded by viral gene 8). During infection, the nucleocapsid penetrates the host plasma membrane and enters the cytosol, whereupon the P8 shell disassembles and the polymerase complex is activated. To understand the molecular mechanisms of shell assembly and disassembly-processes that have counterparts in most viral infections-we have investigated the structure, stability, and dynamics of P8 in different assembly states using time-resolved Raman spectroscopy and hydrogen-isotope exchange. In the presence of Ca(2+), which promotes shell assembly, the highly alpha-helical conformation of the P8 subunit is stabilized by rapid assembly into shell-like structures. However, in the absence of Ca(2+), the P8 subunit is thermolabile and unstable, manifested by a slow alpha-helix --beta-strand conformational change and the accumulation of aberrant aggregates. In both properly assembled shells and aberrant aggregates, the P8 subunit retains an alpha-helical core that is protected against deuterium exchange of amide NH groups. Surprisingly, no additional protection against amide exchange is conferred by the shell lattice. Time-resolved assembly and disassembly experiments in deuterated buffers indicate that the regions of P8 involved in subunit/subunit interactions in the intact shell undergo rapid exchanges, presumably due to local unfolding events that are characterized by low activation barriers. Such localized dynamics of P8 within the shell lattice may mediate the nucleocapsid/host membrane interactions that are required in the cytosol for particle assembly during maturation and disassembly during infection.
- Published
- 1999
41. Purification and characterization of the assembly factor P17 of the lipid-containing bacteriophage PRD1
- Author
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Javier Caldentey, Juha M. Holopainen, Jaana K. H. Bamford, Dennis H. Bamford, Paavo K.J. Kinnunen, and Anna-Liisa Hänninen
- Subjects
Coiled coil ,0303 health sciences ,Leucine zipper ,Viral protein ,Tetrameric protein ,viruses ,030302 biochemistry & molecular biology ,Biology ,medicine.disease_cause ,7. Clean energy ,Biochemistry ,Molecular biology ,Macromolecular assembly ,03 medical and health sciences ,chemistry.chemical_compound ,chemistry ,Tetramer ,Membrane protein ,medicine ,Guanidine ,030304 developmental biology - Abstract
Assembly factors, proteins assisting the formation of viral structures, have been found in many viral systems. The gene encoding the assembly factor P17 of bacteriophage PRD1 has been cloned and expressed in Escherichia coli. P17 acts late in phage assembly, after capsid protein folding and multimerization, and sorting of membrane proteins has occurred. P17 has been purified to near homogeneity. It is a tetrameric protein displaying a rather high heat stability. The protein is largely in an α-helical conformation and possesses a putative leucine zipper which is not essential for protein function, as judged by in vitro mutagenesis and complementation analysis. Although heating does not cause structural changes in the conformation of the protein, the dissociation of the tetramer into smaller units is evident as diminished self-quenching of the fluorescently labeled P17. Similarly, dissociation of the tetramer is also obtained by dialysis of the protein against 6-m guanidine hydrochloride (GdnHCl) or 1% SDS. The reassembly of these smaller units upon cooling is evident from resonance energy transfer.
- Published
- 1999
42. Chlamydia pneumoniae antibodies are associated with an atherogenic lipid profile
- Author
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G. M. L. Ong, Dermot O'Reilly, Liam J. Murray, Alun Evans, K. B. Bamford, and Ciaran O'Neill
- Subjects
Adult ,Male ,Population ,Myocardial Ischemia ,Physiology ,World Health Organization ,chemistry.chemical_compound ,High-density lipoprotein ,Humans ,Medicine ,Risk factor ,education ,education.field_of_study ,Chlamydia ,medicine.diagnostic_test ,business.industry ,Cholesterol ,Incidence ,Incidence (epidemiology) ,Cholesterol, HDL ,Chlamydophila pneumoniae ,Middle Aged ,medicine.disease ,Antibodies, Bacterial ,Lipids ,Cross-Sectional Studies ,chemistry ,Immunoglobulin G ,Chronic Disease ,Papers ,Immunology ,Female ,lipids (amino acids, peptides, and proteins) ,Cardiology and Cardiovascular Medicine ,business ,Lipid profile ,Body mass index ,Biomarkers - Abstract
OBJECTIVE—To determine, within a representative population group of men and women, whether alteration of the lipid profile might underlie the reported association between Chlamydia pneumoniae and ischaemic heart disease. DESIGN AND SETTING—Cross sectional survey in an area with a high incidence of ischaemic heart disease. SUBJECTS—400 randomly selected participants in the World Health Organisation MONICA project's third population survey in Northern Ireland. MAIN OUTCOME MEASURES—Stored sera were examined by microimmunofluorescence for IgG antibodies to C pneumoniae at a dilution of 1 in 64. Mean total and high density lipoprotein (HDL) cholesterol were compared between seropositive and seronegative individuals with adjustment for age, measures of socioeconomic status, smoking habit, alcohol consumption, body mass index, and the season during which blood had been taken. RESULTS—In seropositive men, adjusted mean serum total cholesterol and HDL cholesterol were 0.5 mmol/l (9.2%) higher and 0.11 mmol/l (9.3%) lower, respectively, than in seronegative men. Differences in women did not achieve statistical significance, but both total cholesterol and HDL cholesterol were higher (3.6% and 5.8%, respectively) in seropositive than in seronegative individuals. CONCLUSIONS—There is serological evidence that C pneumoniae infection is associated with an atherogenic lipid profile in men. Altered lipid levels may underlie the association between C pneumoniae and ischaemic heart disease. Keywords: epidemiology; lipids; cholesterol; ischaemic heart disease
- Published
- 1999
43. Irish society of gastroenterology
- Author
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B. M. Ryan, S. McKiernan, P. W. N. Keeling, P. J. Byrne, R. Quill, K. McCallion, R. M. S. Mitchell, R. G. P. Watson, J. S. A. Collins, K. R. Gardiner, D. C. Winter, G. C. O’Sullivan, C. T. Taylor, N. F. Fanning, H. P. Redmond, D. P. O’Donoghue, A. W. Baird, B. J. Harvey, A. E. Brannigan, P. R. O’Connell, M. C. Regan, J. M. Fitzpatrick, R. W. G. Watson, H. Lemass, E. Ryan, P. MacMathuna, J. Crowe, J. C. O’Keane, J. Goh, A. Baird, L. Maher, C. Godson, H. R. Brady, N. A. Petasis, V. V. Fokin, M. K. Barry, D. C. Grant, K. Sheahan, J. M. P. Hyland, K. M. Sheehan, D. J. Fitzgerald, F. E. Murray, A. Heaney, K. B. Bamford, R. J. McFarland, T. C. K. Tham, D. McNamara, S. Franelli, H. Whelan, H. Hamilton, S. Beattie, C. O’Morain, E. G. Brennan, N. O’Hare, R. McDermott, N. I. McDougall, C. M. Gieeson, S. E. H. Russell, J. M. Sloan, D. Morrisey, L. Murphy, B. Kiely, G. Fitzgerald, C. Daly, G. O’Sullivan, F. Shanahan, J. K. Collins, P. Marteau, S. D. Johnston, C. Coates, C. Feighery, J. O’Keeffe, A. Whelan, S. Lynch, D. G. Weir, M. Abuzakouk, L. Barnes, N. O’Gorman, M. McKenna, R. Freaney, M. Young, S. Gaines, D. Brady, D. Drudy, C. O’Farrelly, A. Gilleece, L. Fenelon, J. McPartlin, A. M. Hopkins, A. Myers, P. Moynagh, J. M. Kirby, M. J. Allen, B. Best, H. Calvert, S. Kirk, S. T. D. McKelvey, R. J. Moorehead, J. C. Varghese, S. Sookhai, T. Walsh, H. Osborne, P. Broe, M. J. Lee, D. Moriarty, R. Coffey, E. Murphy, A. A. Shah, E. Murray, B. Thjodleifsson, I. Bjarnason, S. Montague, C. Forkin, G. C. O’Toole, C. M. Gallagher, P. Connell, O. Traynor, T. C. Ling, B. Johnston, M. F. Byrne, M. A. Farrell, C. A. Goulding, S. S. Albloushi, P. O’Connell, L. E. Graham, T. J. Robinson, T. Jabeen, B. Cannon, D. Jenkins, M. J. Whelton, S. Bohra, C. Keohane, M. Duggan, R. K. Siddheshwar, R. G. Wilson, P. J. Hainsworth, F. C. Campbell, S. B. Kelly, B. M. Egan, C. Simutowe, D. A. McNamara, N. Collins, T. N. Walsh, A. Mukherjee, M. Scott, C. Pohl, E. Duggan, M. Wasi, A. Sarkar, L. O. Donnell, P. W. Eustace, J. G. Johnston, R. Waldron, S. Barrett, G. Callagy, J. C. O. Keane, B. Coughlan, J. Sheehan, A. Hickey, A. Carr, M. R. Kell, M. Lynch, D. Ryan, P. Rajpal, W. O. Kirwan, C. J. Larkin, J. E. S. Ardill, K. D. Buchanan, P. L. Lim, M. Gibbons, E. J. Crawford, B. T. Johnston, C. Rodgers, S. Johnston, B. M. Crone, A. H. G. Love, L. Feighery, J. Jackson, M. M. I. Yassin, D. W. Harkin, A. A. B. Barros D’sa, T. G. Parks, M. P. Curry, J. E. Hegarty, L. Golden-Mason, E. Hannigan, and N. Parfrey
- Subjects
medicine.medical_specialty ,Pediatrics ,Irish ,business.industry ,Family medicine ,medicine ,language ,General Medicine ,business ,language.human_language - Published
- 1998
44. Irish society of gastroenterology
- Author
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G. Clarke, E. Ryan, J. C. O’Keane, J. Crowe, P. McMathuna, D. Moriarty, R. Ettarh, K. Sheahan, J. Hyland, D. P. O’Donoghue, A. W. Baird, G. Gormley, J. C. O. Keane, P. MacMathuna, J. H. Wang, Q. D. Wu, H. P. Redmond, C. Condron, D. Bouchier-Hayes, K. Nally, F. Newton, J. O’Connell, G. C. O’Sullivan, J. Morgan, J. K. Collins, F. Shanahan, C. Goode, D. C. Winter, C. T. Taylor, M. M. Skelly, B. J. Harvey, J. C. Varghese, M. A. Farrell, F. P. McGrath, F. E. Murray, H. Osborne, M. J. Lee, A. Sullivan, A. E. Ryan, A. N. Donovan, P. A. McCormick, B. Kenny, S. Somers, A. Bohan, R. G. Gibney, M. Marcaccio, D. E. Malone, M. Doyle, C. P. Delaney, T. F. Gorey, G. P. McEntee, A. Clarke, R. Stuart, J. Kelly, M. D. Kiely, M. O’Sullivan, E. Lovett, N. Mahmud, D. Kelleher, C. A. O’Morain, C. J. Larkin, R. G. P. Watson, J. M. Sloan, J. E. S. Ardill, C. F. Johnston, K. D. Buchanan, A. Heaney, J. S. A. Collins, G. R. P. Watson, R. M. Kalin, T. C. K. Tham, R. J. McFarland, K. B. Bamford, T. Ó Cróinín, M. Clyne, B. Drumm, M. Rowland, D. Kumar, P. O’Connor, L. E. Daly, D. L. O’Toole, A. Long, A. M. Murphy, L. O’Neill, D. G. Weir, A. M. Hopkins, P. Moynagh, C. Brennan, J. Harmey, P. P. Stapleton, A. M. Rasheed, G. Chen, C. Kelly, D. J. Bouchier-Hayes, A. Leahy, M. Gallagher, A. Grace, Y. Xin, M. Leader, E. Kay, A. Whelan, U. Pattison, R. Willoughby, E. Wallace, D. Weir, C. Feighery, M. W. Bennett, C. Brady, D. Roche, A. Molloy, J. McPartlin, J. M. Scott, A. G. Acheson, J. Lee, K. Khosraviani, S. T. Irwin, J. McDaid, J. R. Docherty, A. O’Grady, M. Mabruk, C. Johnston, W. Curry, J. Ardill, R. Cunningham, N. I. McDougall, P. V. Coyle, M. E. Callender, A. M. Ouinn, R. Warner, F. M. Stevens, P. I. S. Chakravarthi, M. Kearns, M. Bourke, A. Hassan, J. McWeeney, C. F. McCarthy, M. Casey, J. O’Donoghue, A. M. Eustace-Ryan, P. O’Regan, L. Feighery, J. Jackson, N. Cronin, K. Quane, E. D. Mulligan, T. Purcell, B. Dunne, M. Griffin, N. Noonan, D. Hollywood, N. Keeling, J. V. Reynolds, T. P. J. Hennessy, M. O’Sulhvan, I. Harman, N. P. Breslin, N. Clayton, S. Hogan, B. Donovan, D. Hayes, M. Kiely, C. A. Goulding, S. S. Albloushi, J. O’Connor, M. G. Courtney, D. Royston, A. G. Shattock, A. Stack, M. Carmody, S. Barrett, A. Hennigan, L. Young, C. J. Shields, C. O’Keane, J. M. Fitzpatrick, M. M. Doyle, R. B. Stephens, P. A. Daly, G. M. Briggs, D. McCrory, S. O’Neill, H. O’Grady, D. C. Grant, K. Barry, O. Traynor, J. M. P. Hyland, G. C. O’Toole, M. K. Barry, S. D. Johnston, C. M. Ritchie, T. J. Robinson, J. M. Kirby, E. M. Mackle, N. Haider, N. Aherne, F. McNichol, D. Hamilton, P. Neary, S. Hegarty, J. O. Connor, R. G. K. Watson, D. Drudy, A. Alwan, L. Fenelon, C. O’Farrelly, B. Byrne, L. Madrigal, J. Carton, C. Collins, D. O’Donoghue, N. Gannon, A. Hickey, C. A. O’Boyle, R. Byrne, S. Albloushi, and F. Murray
- Subjects
medicine.medical_specialty ,Irish ,business.industry ,Ophthalmology ,language ,Library science ,Medicine ,General Medicine ,business ,language.human_language - Published
- 1998
45. The IncP plasmid-encoded cell envelope-associated DNA transfer complex increases cell permeability
- Author
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A. M. Grahn, Jaana K. H. Bamford, Dennis H. Bamford, E. Lanka, and Rimantas Daugelavičius
- Subjects
DNA, Bacterial ,Cell Membrane Permeability ,Biology ,Microbiology ,Membrane Potentials ,03 medical and health sciences ,chemistry.chemical_compound ,Adenosine Triphosphate ,Onium Compounds ,Organophosphorus Compounds ,Plasmid ,Bacterial Proteins ,Escherichia coli ,Molecular Biology ,reproductive and urinary physiology ,030304 developmental biology ,Membrane potential ,0303 health sciences ,urogenital system ,030306 microbiology ,DNA transport ,Temperature ,Membrane Proteins ,chemistry ,Biochemistry ,Conjugation, Genetic ,Potassium ,Biophysics ,Receptors, Virus ,Cell envelope ,Adenosine triphosphate ,Intracellular ,DNA ,Plasmids ,Tectiviridae ,Research Article ,MPF complex - Abstract
IncP-type plasmids are broad-host-range conjugative plasmids. DNA translocation requires DNA transfer-replication functions and additional factors required for mating pair formation (Mpf). The Mpf system is located in the cell membranes and is responsible for DNA transport from the donor to the recipient. The Mpf complex acts as a receptor for IncP-specific phages such as PRD1. In this investigation, we quantify the Mpf complexes on the cell surface by a phage receptor saturation technique. Electrochemical measurements are used to show that the Mpf complex increases cell envelope permeability to lipophilic compounds and ATP. In addition it reduces the ability of the cells to accumulate K+. However, the Mpf complex does not dissipate the membrane voltage. The Mpf complex is rapidly disassembled when intracellular ATP concentration is decreased, as measured by a PRD1 adsorption assay.
- Published
- 1997
46. Epidemiology of Helicobacter pylori infection among 4742 randomly selected subjects from Northern Ireland
- Author
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E E McCrum, K. B. Bamford, Alun Evans, and Liam J. Murray
- Subjects
Adult ,Male ,medicine.medical_specialty ,Adolescent ,Alcohol Drinking ,Epidemiology ,Population ,Northern Ireland ,Body Mass Index ,Helicobacter Infections ,Serology ,Random Allocation ,Sex Factors ,Risk Factors ,Internal medicine ,Prevalence ,Humans ,Medicine ,Serologic Tests ,Risk factor ,Child ,education ,education.field_of_study ,Helicobacter pylori ,biology ,business.industry ,Smoking ,Age Factors ,General Medicine ,Odds ratio ,Middle Aged ,biology.organism_classification ,Health Surveys ,Body Height ,Confidence interval ,Social Class ,Immunology ,Female ,business ,Body mass index - Abstract
Background. Despite the widespread prevalence and serious clinical sequelae of infection with Helicobacter pylori, there have been few large population-based studies, using randomly selected subjects, examining the epidemiology of this infection. Aim. To examine the distribution and determinants of H. pylon infection in a developed country. Subjects and Setting. Overall 4742 subjects, aged 12-64, from Northern ireland were randomly selected. Methods. Helicobacter pylori specific IgG antibodies were measured by enzyme linked immunosorbent assay, using an acid-glycine extract antigen, in stored serum from subjects who had participated in three linked population-based surveys of cardiovascular risk factors performed in 1986 and 1987. Results. The overall prevalence of H. pylori infection was 50.5%. Prevalence increased with age from 23.4% in 12-14 year olds to 72.7% in 60-64 year olds: chi(2) for trend 518, P < 10(-4). In subjects aged greater than or equal to 25, infection was more common in males (60.9%) than females (55.2%):;chi(2) = 9.53, P < 0.01. This relation remained significant after adjusting for age, and measures of socioeconomic class: odds ratio (OR) for infection, male versus female was 1.19 (95% confidence interval [CI] : 1.02-1.40). infection was associated with social class: the adjusted OR of infection in subjects from manual social classes relative to those from non-manual classes was 1.7 (95% Ci : 1.47-1.98). Infection was significantly more common in current smokers and ex-smokers than in subjects who had never smoked: adjusted OR for infection, ex-smokers versus never smoked was 1.22 (95% CI : 1.01-1.49); for smokers of greater than or equal to 20/day versus never smoked OR = 1.33 (95% CI:1.05-1.67). Infection was not associated with height in adult males but mean height in infected women was lower than in uninfected women after adjusting for age and socioeconomic status: difference in mean height (SE), -0.85 cm (0.32), P < 0.01. There was no demonstrable relationship between H. pylori infection and current alcohol intake. Conclusions. This study demonstrated a high prevalence of infection in a population from a developed country. Previously reported associations between H. pylori infection, age, sex, social class, and reduced height in females were confirmed and smoking was identified asa possible risk factor for H. pylori infection.
- Published
- 1997
47. Polarized Raman spectroscopy of double-stranded RNA from bacteriophage phi6: local Raman tensors of base and backbone vibrations
- Author
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Masamichi Tsuboi, J. K. H. Bamford, George J. Thomas, and James M. Benevides
- Subjects
inorganic chemicals ,Quantitative Biology::Biomolecules ,Molecular Structure ,Chemistry ,technology, industry, and agriculture ,Biophysics ,Stacking ,Context (language use) ,Deuterium ,Spectrum Analysis, Raman ,Quantitative Biology::Genomics ,Biophysical Phenomena ,Bacteriophage phi 6 ,Z-DNA ,symbols.namesake ,Crystallography ,Molecular vibration ,Helix ,symbols ,Nucleic acid ,RNA, Viral ,Raman spectroscopy ,Protein secondary structure ,RNA, Double-Stranded ,Research Article - Abstract
Raman tensors for localized vibrations of base (A, U, G, and C), ribose and phosphate groups of double-stranded RNA have been determined from polarized Raman measurements on oriented fibers of the genomic RNA of bacteriophage phi6. Polarized Raman intensities for which electric vectors of both the incident and scattered light are polarized either perpendicular (I[bb]) or parallel (I[cc]) to the RNA fiber axis have been obtained by Raman microspectroscopy using 514.5-nm excitation. Similarly, the polarized Raman components, I(bc) and I(cb), for which incident and scattered vectors are mutually perpendicular, have been obtained. Spectra collected from fibers maintained at constant relative humidity in both H2O and D2O environments indicate the effects of hydrogen-isotopic shifts on the Raman polarizations and tensors. Novel findings are the following: 1) the intense Raman band at 813 cm(-1), which is assigned to phosphodiester (OPO) symmetrical stretching and represents the key marker of the A conformation of double-stranded RNA, is characterized by a moderately anisotropic Raman tensor; 2) the prominent RNA band at 1101 cm(-1), which is assigned to phosphodioxy (PO2-) symmetrical stretching, also exhibits a moderately anisotropic Raman tensor. Comparison with results obtained previously on A, B, and Z DNA suggests that tensors for localized vibrations of backbone phosphodiester and phosphodioxy groups are sensitive to helix secondary structure and local phosphate group environment; and 3) highly anisotropic Raman tensors have been found for prominent and well-resolved Raman markers of all four bases of the RNA duplex. These enable the use of polarized Raman spectroscopy for the determination of purine and pyrimidine base residue orientations in ribonucleoprotein assemblies. The present determination of Raman tensors for dsRNA is comprehensive and accurate. Unambiguous tensors have been deduced for virtually all local vibrational modes of the 300-1800 cm(-1) spectral interval. The results provide a reliable basis for future evaluations of the effects of base pairing, base stacking, and sequence context on the polarized Raman spectra of nucleic acids.
- Published
- 1997
48. Assembly of Membrane-Containing Bacteriophage PRD1 Is Dependent on GroEL and GroES
- Author
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Anna-Liisa Hänninen, Jaana K. H. Bamford, and Dennis H. Bamford
- Subjects
Protein Folding ,viruses ,macromolecular substances ,Chaperonin ,Viral Proteins ,03 medical and health sciences ,Bacteriophage PRD1 ,Virology ,Chaperonin 10 ,Escherichia coli ,030304 developmental biology ,0303 health sciences ,biology ,Virus Assembly ,030302 biochemistry & molecular biology ,Chaperonin 60 ,GroES ,Molecular biology ,GroEL ,3. Good health ,enzymes and coenzymes (carbohydrates) ,Membrane ,Capsid ,Chaperone (protein) ,Mutation ,biological sciences ,Foldase ,biology.protein ,Biophysics ,bacteria ,Tectiviridae - Abstract
Assembly of the broad-host-range bacteriophage PRD1 involves translocation of the virus-specific membrane to the inside of the icosahedral protein shell formed of trimeric coat proteins. The formation of PRD1 particles is, in addition to the virus-encoded assembly factors P10 and P17, dependent on GroEL/GroES chaperonins. The chaperonins assist in the folding of the capsid proteins P3 and P5 and in the assembly of viral membrane proteins.
- Published
- 1997
49. Probing Phage PRD1-Specific Proteins with Monoclonal and Polyclonal Antibodies
- Author
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Jaana K. H. Bamford, Dennis H. Bamford, and Anna-Liisa Hänninen
- Subjects
Salmonella typhimurium ,viruses ,Genome, Viral ,medicine.disease_cause ,Antibodies, Viral ,03 medical and health sciences ,Viral Proteins ,Capsid ,Antibody Specificity ,Virology ,medicine ,Escherichia coli ,Cloning, Molecular ,Gene ,030304 developmental biology ,Infectivity ,Antiserum ,0303 health sciences ,biology ,030302 biochemistry & molecular biology ,Antibodies, Monoclonal ,Molecular biology ,3. Good health ,Polyclonal antibodies ,Monoclonal ,biology.protein ,Capsid Proteins ,Antibody ,Tectiviridae - Abstract
Four new specificity class MAbs against PRD1 proteins (P6, P7/14, P11, P18) and polyclonal antiserum against the minor capsid protein P5 were produced. The antibodies were used to analyze the phage protein distribution inside the host cell during infection as well as in the virion. The minor component of the capsid, P5, was shown to be located on the surface of the virion. The proteins responsible for particle infectivity were localized to the membrane fraction of the host cells. In addition, by detection with MAbs, genes encoding proteins P14 and P18 were positively localized on the PRD1 genome.
- Published
- 1997
- Full Text
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50. Bacteriophage P23-77 capsid protein structures reveal the archetype of an ancient branch from a major virus lineage
- Author
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Sari Mäntynen, Karl Harlos, Jaana K. H. Bamford, Alice Pawlowski, Jonathan M. Grimes, Ilona Rissanen, and David I. Stuart
- Subjects
Models, Molecular ,Protein Conformation ,Viral protein ,Lineage (evolution) ,viruses ,Crystallography, X-Ray ,medicine.disease_cause ,Article ,Virus ,Viral Assembly ,Bacteriophage ,03 medical and health sciences ,Protein structure ,Structural Biology ,medicine ,Bacteriophages ,Molecular Biology ,030304 developmental biology ,Sequence (medicine) ,0303 health sciences ,biology ,030306 microbiology ,Cryoelectron Microscopy ,ta1183 ,ta1182 ,biology.organism_classification ,Virology ,3. Good health ,Capsid ,Evolutionary biology ,Capsid Proteins ,Crystallization - Abstract
Summary It has proved difficult to classify viruses unless they are closely related since their rapid evolution hinders detection of remote evolutionary relationships in their genetic sequences. However, structure varies more slowly than sequence, allowing deeper evolutionary relationships to be detected. Bacteriophage P23-77 is an example of a newly identified viral lineage, with members inhabiting extreme environments. We have solved multiple crystal structures of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. They fit the 14 Å resolution cryo-electron microscopy reconstruction of the entire virus exquisitely well, allowing us to propose a model for both the capsid architecture and viral assembly, quite different from previously published models. The structures of the capsid proteins and their mode of association to form the viral capsid suggest that the P23-77-like and adeno-PRD1 lineages of viruses share an extremely ancient common ancestor., Highlights • High-resolution structures of the two major capsid proteins of bacteriophage P23-77 • P23-77 capsid proteins exhibit a conserved single β-barrel core fold • P23-77 is an ancient relative of the double β-barrel lineage of viruses • Capsid model illustrates that P23-77 uses a novel method of organization, Rissanen et al. propose a model for the architecture and assembly of bacteriophage P23-77 quite different from those previously published. The capsid proteins and their mode of association to form the virus particle suggest that P23-77 share a common evolutionary origin with the PRD1/Adenovirus lineage.
- Published
- 2013
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