The folding of an organism's DNA molecule into a compact, orderly structure that fits within the limited space of a CELL or VIRUS PARTICLE.
Viruses whose host is Bacillus. Frequently encountered Bacillus phages include bacteriophage phi 29 and bacteriophage phi 105.
Viruses whose hosts are bacterial cells.
Deoxyribonucleic acid that makes up the genetic material of viruses.
The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.
Bacteriophage in the genus T7-like phages, of the family PODOVIRIDAE, which is very closely related to BACTERIOPHAGE T7.
A temperate inducible phage and type species of the genus lambda-like viruses, in the family SIPHOVIRIDAE. Its natural host is E. coli K12. Its VIRION contains linear double-stranded DNA with single-stranded 12-base 5' sticky ends. The DNA circularizes on infection.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
Proteins found in any species of virus.
Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.
Viruses whose host is Escherichia coli.
Viruses whose host is Salmonella. A frequently encountered Salmonella phage is BACTERIOPHAGE P22.
Form in which product is processed or wrapped and labeled. PRODUCT LABELING is also available.
A group of enzymes catalyzing the endonucleolytic cleavage of DNA. They include members of EC 3.1.21.-, EC 3.1.22.-, EC 3.1.23.- (DNA RESTRICTION ENZYMES), EC 3.1.24.- (DNA RESTRICTION ENZYMES), and EC 3.1.25.-.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Viruses whose host is Streptococcus.
The phenomenon by which a temperate phage incorporates itself into the DNA of a bacterial host, establishing a kind of symbiotic relation between PROPHAGE and bacterium which results in the perpetuation of the prophage in all the descendants of the bacterium. Upon induction (VIRUS ACTIVATION) by various agents, such as ultraviolet radiation, the phage is released, which then becomes virulent and lyses the bacterium.
Containers, packaging, and packaging materials for processed and raw foods and beverages. It includes packaging intended to be used for storage and also used for preparation of foods such as microwave food containers versus COOKING AND EATING UTENSILS. Packaging materials may be intended for food contact or designated non-contact, for example, shipping containers. FOOD LABELING is also available.
A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.
Containers, packaging, and packaging materials for drugs and BIOLOGICAL PRODUCTS. These include those in ampule, capsule, tablet, solution or other forms. Packaging includes immediate-containers, secondary-containers, and cartons. In the United States, such packaging is controlled under the Federal Food, Drug, and Cosmetic Act which also stipulates requirements for tamper-resistance and child-resistance. Similar laws govern use elsewhere. (From Code of Federal Regulations, 21 CFR 1 Section 210, 1993) DRUG LABELING is also available.
The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Proteins that are involved in or cause CELL MOVEMENT such as the rotary structures (flagellar motor) or the structures whose movement is directed along cytoskeletal filaments (MYOSIN; KINESIN; and DYNEIN motor families).
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Proteins that form the CAPSID of VIRUSES.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.
Electron microscopy involving rapid freezing of the samples. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains.
Viruses whose nucleic acid is DNA.
Bacteriophage and type species in the genus Tectivirus, family TECTIVIRIDAE. They are specific for Gram-negative bacteria.
A species of temperate bacteriophage in the genus P22-like viruses, family PODOVIRIDAE, that infects SALMONELLA species. The genome consists of double-stranded DNA, terminally redundant, and circularly permuted.
Ribonucleic acid that makes up the genetic material of viruses.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
The functional hereditary units of VIRUSES.
A species of temperate bacteriophage in the genus P2-like viruses, family MYOVIRIDAE, which infects E. coli. It consists of linear double-stranded DNA with 19-base sticky ends.
The process by which a DNA molecule is duplicated.
Viruses whose host is Pseudomonas. A frequently encountered Pseudomonas phage is BACTERIOPHAGE PHI 6.
Bacteriophages whose genetic material is RNA, which is single-stranded in all except the Pseudomonas phage phi 6 (BACTERIOPHAGE PHI 6). All RNA phages infect their host bacteria via the host's surface pili. Some frequently encountered RNA phages are: BF23, F2, R17, fr, PhiCb5, PhiCb12r, PhiCb8r, PhiCb23r, 7s, PP7, Q beta phage, MS2 phage, and BACTERIOPHAGE PHI 6.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.
A species of gram-positive bacteria that is a common soil and water saprophyte.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.
Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.
A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.
The type species of SIMPLEXVIRUS causing most forms of non-genital herpes simplex in humans. Primary infection occurs mainly in infants and young children and then the virus becomes latent in the dorsal root ganglion. It then is periodically reactivated throughout life causing mostly benign conditions.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Viral proteins that are components of the mature assembled VIRUS PARTICLES. They may include nucleocapsid core proteins (gag proteins), enzymes packaged within the virus particle (pol proteins), and membrane components (env proteins). These do not include the proteins encoded in the VIRAL GENOME that are produced in infected cells but which are not packaged in the mature virus particle,i.e. the so called non-structural proteins (VIRAL NONSTRUCTURAL PROTEINS).
The transfer of bacterial DNA by phages from an infected bacterium to another bacterium. This also refers to the transfer of genes into eukaryotic cells by viruses. This naturally occurring process is routinely employed as a GENE TRANSFER TECHNIQUE.
The development of anatomical structures to create the form of a single- or multi-cell organism. Morphogenesis provides form changes of a part, parts, or the whole organism.
Viruses whose host is one or more Mycobacterium species. They include both temperate and virulent types.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Specific loci on both the bacterial DNA (attB) and the phage DNA (attP) which delineate the sites where recombination takes place between them, as the phage DNA becomes integrated (inserted) into the BACTERIAL DNA during LYSOGENY.
Established cell cultures that have the potential to propagate indefinitely.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
A subdiscipline of genetics which deals with the genetic mechanisms and processes of microorganisms.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by complex contractile tails.
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
Viruses which enable defective viruses to replicate or to form a protein coat by complementing the missing gene function of the defective (satellite) virus. Helper and satellite may be of the same or different genus.
A technique of bacterial typing which differentiates between bacteria or strains of bacteria by their susceptibility to one or more bacteriophages.
Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Virulent bacteriophage and sole member of the genus Cystovirus that infects Pseudomonas species. The virion has a segmented genome consisting of three pieces of doubled-stranded DNA and also a unique lipid-containing envelope.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
A non-pathogenic species of LACTOCOCCUS found in DAIRY PRODUCTS and responsible for the souring of MILK and the production of LACTIC ACID.
Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.
Rupture of bacterial cells due to mechanical force, chemical action, or the lytic growth of BACTERIOPHAGES.
Electron microscopy in which the ELECTRONS or their reaction products that pass down through the specimen are imaged below the plane of the specimen.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
Species of the genus MASTADENOVIRUS, causing a wide range of diseases in humans. Infections are mostly asymptomatic, but can be associated with diseases of the respiratory, ocular, and gastrointestinal systems. Serotypes (named with Arabic numbers) have been grouped into species designated Human adenovirus A-F.
An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.
A family of bacteriophages which are characterized by short, non-contractile tails.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
An antibiotic first isolated from cultures of Streptomyces venequelae in 1947 but now produced synthetically. It has a relatively simple structure and was the first broad-spectrum antibiotic to be discovered. It acts by interfering with bacterial protein synthesis and is mainly bacteriostatic. (From Martindale, The Extra Pharmacopoeia, 29th ed, p106)
The rate dynamics in chemical or physical systems.
A genus of filamentous bacteriophages of the family INOVIRIDAE. Organisms of this genus infect enterobacteria, PSEUDOMONAS; VIBRIO; and XANTHOMONAS.
A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.
A CELL LINE derived from the kidney of the African green (vervet) monkey, (CERCOPITHECUS AETHIOPS) used primarily in virus replication studies and plaque assays.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)
The sum of the weight of all the atoms in a molecule.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
A temperate coliphage, in the genus Mu-like viruses, family MYOVIRIDAE, composed of a linear, double-stranded molecule of DNA, which is able to insert itself randomly at any point on the host chromosome. It frequently causes a mutation by interrupting the continuity of the bacterial OPERON at the site of insertion.
The adhesion of gases, liquids, or dissolved solids onto a surface. It includes adsorptive phenomena of bacteria and viruses onto surfaces as well. ABSORPTION into the substance may follow but not necessarily.
Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.
Proteins found in any species of bacterium.
Catalano, C. E.; Cue, D.; Feiss, M. (1995). "Virus DNA packaging: the strategy used by phage λ". Molecular Microbiology. 16 (6 ... Production and assembly of stable proheads is an essential precursor to bacteriophage genome packaging; this packaging activity ... as seen with the prohead of Bacillus subtilis phage φ29. ...
Becker, A; Murialdo, H; Gold, M (1977). "Studies on an in Vitro System for the Packaging and Maturation of Phage Lambda DNA". ... Casjens, S (1994). "DNA packaging by lambdoid phages - From pure beginnings to applications in genetic engineering". BioEssays ... "Studies on an in Vitro System for the Packaging and Maturation of Phage Lambda DNA". Virology. 78 (1): 277-290. doi:10.1016/ ... Murialdo, H (1991). "Bacteriophage Lambda DNA Maturation and Packaging". Annu. Rev. Biochem. 60: 125-153. doi:10.1146/annurev. ...
Strauss H, King J (February 1984). "Steps in the stabilization of newly packaged DNA during phage P22 morphogenesis". J. Mol. ... It is a temperate double stranded DNA phage as well as a lambdoid phage since it carries control of gene expression regions and ... so part of the host DNA is transferred along with the phage. After host infection, the linear P22 virion DNA is circularized by ... The P22 packaged DNA carries a direct duplication of about 4% at both ends since the inside of the virion has more space than ...
The insert DNA is replicated with the viral DNA; thus, together they are packaged into viral particles. These particles are ... Phage λ is a double-stranded DNA virus that infects E. coli. The λ chromosome is 48.5kb long and can carry inserts up to 25kb. ... They begin as linear DNA molecules packaged into bacteriophage P1 particles. These particles are injected into an E. coli ... The DNA is stored in a population of identical vectors, each containing a different insert of DNA. In order to construct a ...
While somewhat similar to a transducing particle, GTAs are not created by accident when a phage is packaging DNA into viral ... The DNA packaged in the particles is also random; it does not contain all the genes needed for GTA production. ... A gene transfer agent (GTA) is a phage-like particle that transfers small amounts of DNA from the producing cell's chromosome ... This DNA exchange was still observed even when cell contact was eliminated and DNases were added which allowed them to rule out ...
The ligation mix is then packaged into phage particles and the DNA is transfected into the bacterial host. Bacterial clones ... Fosmids can hold DNA inserts of up to 40 kb in size; often the source of the insert is random genomic DNA. A fosmid library is ... Fosmids are DNA vectors that use the F-plasmid origin of replication and partitioning mechanisms to allow cloning of large DNA ... There are now many companies that can create a fosmid library from any sample of DNA in a very short period of time at a ...
This phagemid DNA is then packaged into phage particles. The phage particles containing ssDNA are released from the bacterial ... provides the necessary viral components to enable single stranded DNA replication and packaging of the phagemid DNA into phage ... contrasting with the lambda phage and the T7 phage, are not generally lytic. Helper phages are usually engineered to package ... "Phage Display". A phagemid(plasmid +phage) is a plasmid that contains an f1 origin of replication from an f1 phage. It can be ...
Serwer, P; Wright, ET; Hakala, K; Weintraub, ST; Su, M; Jiang, W (Mar 26, 2010). "DNA packaging-associated hyper-capsid ... This phage is closely related to T7 phage in structure though the two viruses may differ in capsid maturation. FRASER, D; ... T3+Phage at the US National Library of Medicine Medical Subject Headings (MeSH) v t e. ... Escherichia virus T3, also called bacteriophage T3 and T3 phage, is a bacteriophage capable of infecting susceptible bacterial ...
Synthesis of infectious phage phi-X174 DNA". Proceedings of the National Academy of Sciences of the United States of America. ... ssDNA genomes to package into viruses are created from this by a rolling circle mechanism. This is the mechanism by which the ... The phi X 174 (or ΦX174) bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli, and the first DNA- ... and more distantly related to the G4-like phages and even more distantly related to the α3-like phage. Rokyta et al. 2006 ...
"Staphylococcal pathogenicity island DNA packaging system involving cos-site packaging and phage-encoded HNH endonucleases". ... April 2009). "Specificity of staphylococcal phage and SaPI DNA packaging as revealed by integrase and terminase mutations". ... and packaging. They lack structural phage proteins and lysis proteins and utilize those of the helper phage , which they modify ... the SaPIs are major agents of phage-dependent HGT, as they only partially block phage reproduction and also package chromosomal ...
Phage P2 has a double stranded DNA genome packaged in an icosahedral capsid with a diameter of 60 nanometers that is connected ... which is essential for the following phage binding and injection of phage DNA . During the adsorption process, the tail fiber ... Presence of phage P4 can cause P2 to form smaller capsids. The tail ends in a baseplate which is the control hub for phage ... This genus of viruses includes many P2-like phages as well as the satellite phage P4. Bacteriophage P2 was first isolated by G ...
Phage libraries are also stored and screened more easily than cosmid libraries. Target DNA: the genomic DNA to be cloned has to ... the vector without insert DNA will not be packaged ( Plasmids instability is increased if the novel inserted DNA contains many ... The DNA must be linear to fit into a phage head.) The cosB site holds the terminase while it is nicking and separating the ... Unlike plasmids, they can also be packaged in vitro into phage capsids, a step which requires cohesive ends, also known as cos ...
The genomes of these phages are linear double stranded DNA (~40kilobases), terminally redundant and circularly permuted. ... packaging, morphogenesis, lysis and integration). Genomes are around 40kb in length. Viral replication is cytoplasmic. Entry ... These phages are temperate and infect Salmonella (Salmonella virus Epsilon15) and Escherichia coli (Escherichia phage PhiV10). ... Dna templated transcription is the method of transcription. Bacteria serve as the natural host. Transmission routes are passive ...
... hence blocks phage TerS/TerL complex formation responsible for phage DNA packaging. In second mechanism PICI CpmAB redirect the ... phage capsid morphogenetic protein to make 95% of SaPI-sized capsid and phage DNA can package only 1/3rd of their genome in ... The type III systems analysed from S. solfataricus and P. furiosus both target the mRNA of phages rather than phage DNA genome ... In 2005, three independent research groups showed that some CRISPR spacers are derived from phage DNA and extrachromosomal DNA ...
"In vitro packaging of a λ Dam vector containing EcoRI DNA fragments of Escherichia coli and phage P1", Gene, 1 (3-4): 255-80, ... DNA methylation and viral packaging, as well as immunity to the phage. He and his coworkers also developed P1-derived cloning ... From 1981 he directed his own group, continuing to research the P1 phage, as well as branching out to study DNA recombination ... particularly known for his work on DNA recombination and the phage P1. Born in 1942 in Brooklyn, New York, Sternberg gained a ...
The packaging of bacteriophage DNA into phage capsids has low fidelity. Small pieces of bacterial DNA may be packaged into the ... It happens when a phage is in the lytic stage, at the moment that the viral DNA is packaged into phage heads. If the virus ... When the bacterial DNA packaged into the virus is inserted into the recipient cell three things can happen to it: The DNA is ... The excised DNA is then packaged into a new virus particle, which then delivers the DNA to a new bacterium. Here, the donor ...
Fosmids are a hybrid between bacterial F plasmids and λ phage cloning techniques. Inserts are pre-packaged into phage particles ... A DNA construct is an artificially-designed segment of DNA borne on a vector that can be used to incorporate genetic material ... A DNA construct contains a DNA insert, called a transgene, delivered via a transformation vector which allows the insert ... DNA constructs are widely adapted in molecular biology research for techniques such as DNA sequencing, protein expression, and ...
Similar DNA packaging exists also in chloroplasts and mitochondria. Bacterial DNA is sometimes referred to as the bacterial ... This packing can change from hexagonal to cholesteric to isotropic at different stages of the phage functioning. Although the ... DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are ... and salt is required to neutralize DNA charges and decrease DNA-DNA repulsion. The second possibility can be realized by ...
Replication follows the DNA strand displacement model. DNA-templated transcription is the method of transcription. Bacteria ... Another virus (Weissella phage phiYS61) that has been isolated is so unlike the known members that it may belong to a new genus ... Picoviruses package linear, monomeric genomes with a terminal protein covalently attached to each end. Viral replication is ... They also use a typical protein primed DNA polymerase for replication, a property shared with the family Tectiviridae.[citation ...
... coli cells until they are infected with helper phage, which enables packaging of the phage DNA and assembly of the mature ... This phage-display library is added to the dish and after allowing the phage time to bind, the dish is washed. Phage-displaying ... Loss of phage infectivity can be avoided by using a phagemid plasmid and a helper phage so that the resultant phage contains ... Attached phage may be eluted and used to create more phage by infection of suitable bacterial hosts. The new phage constitutes ...
Packaging cannot occur from circular phage DNA, only from concatomeric DNA. Q is similar to N in its effect: Q binds to RNA ... The original B-O-B' sequence is changed by the integration to B-O-P'-phage DNA-P-O-B'. The phage DNA is now part of the host's ... Soon, the phage switches to a rolling circle replication similar to that used by phage M13. The DNA is nicked and the 3' end ... During infection, the phage particle recognizes and binds to its host, E. coli, causing DNA in the head of the phage to be ...
... mechanism of switch from DNA replication to DNA packaging" Cell 47(1) 99-106 Hafenstein S and Fane BA (2002) X174 Genome-capsid ... Enterobacteria phage alpha3 Enterobacteria phage G4 Enterobacteria phage phiK Enterobacteria phage phiX174 Enterobacteria phage ... Chlamydia phage 1 Chlamydia phage 2 Chlamydia pneumoniae phage CPAR39 Guinea pig Chlamydia phage Genus: Spiromicrovirus ... The host's DNA polymerase converts the single-stranded DNA into double-stranded DNA. 6. Late genes are now transcribed by the ...
The DNA is packaged and stored in the protein head of the phage in a linear fashion. But after infecting cells the linear ... As T5-Like phages refers to the morphology of the phage, or the structure and outward appearance. Some of the T5-Like phages ... potentially DNA primase, and a few others that are only hypothesized. Mycobacterium virus D29 is a big DNA phage, this just ... Lysis is a procedure in which after the phage has irreversibly attached to the cell and injected its DNA into the host, and ...
Pruss, G; Goldstein, RN; Calendar, R (June 1974). "In vitro packaging of satellite phage P4 DNA". Proceedings of the National ... The P4 virion has a tail and an icosahedral head containing a linear double-stranded DNA genome of 11,627 kb. Phage P4 infects ... Enterobacteria phage P4 (also known as satellite phage P4) is a temperate bacteriophage strain of species Escherichia virus P2 ... It is a satellite virus which cannot engage in lytic growth without the presence of a P2-related helper phage. It generally ...
DNA molecules can be packaged, since more (or fewer) p8 subunits can be added during assembly as required to protect the DNA, ... Replication of RF DNA is converted to production of phage ssDNA by coating of the DNA with p5 to form an elongated p5/DNA ... Ff phages (for F specific filamentous phages) is a group of almost identical filamentous phage (genus Inovirus) including f1, ... which are necessary for further DNA replication. The p2 protein cleaves the viral strand of the RF DNA, and host DNA polymerase ...
The tail sheath contracts and the DNA of the phage is injected into the host cell. The host DNA recombination machinery or the ... The end of the concatemer is cut a specific site called the pac site or packaging site. This is followed by the packing of the ... the lambda phage) that integrate into the host DNA. P1 has an icosahedral head containing the DNA attached to a contractile ... The P1 phage has gained research interest because it can be used to transfer DNA from one bacterial cell to another in a ...
During fd phage assembly, the phage DNA is first packaged into a linear intracellular nucleoprotein complex with many copies of ... although they are not present in the phage DNA) and to similar hairpin structures in phage DNA. The p1 protein of Ff phage (i. ... species Thermus phage PH75 PH75 phage species Xanthomonas phage Cf1t (likely misspelled as Cflt) Cf1t phage The filamentous ... This topology was assumed to extend to all other filamentous phages, but it is not the case for phage Pf4, for which the DNA in ...
... and the genes for DNA packaging. The phage genes specifying its regulation and DNA replication have typically been deleted, and ... The DNA packaging machinery then packs DNA into each head, cutting the DNA when the head is full, attaching a tail to the head ... packaging of short DNA fragments (4.2 kb) and regulation by quorum sensing and a CtrA phosphorelay. However, its DNA packaging ... Dd1 packages 13.6 kb DNA fragments M. voltae is an archaean; its GTA is known to transfer 4.4 kb DNA fragments but has not been ...
First press stories on DNA but for the 'second' DNA story in The New York Times, see: ... Phage workers. *Recipients of the Copley Medal. *Royal Medal winners. *Sleep researchers ... At any rate he was preoccupied with proteins at the time, not DNA.[39][40] Watson and Crick were not officially working on DNA ... Her identification of the space group for DNA crystals revealed to Crick that the DNA strands were antiparallel, which helped ...
VVPPs will have evolved mechanisms of DNA insertion and replication that manipulate eukaryotic surface proteins and DNA editing ... "Package Insert - LUXTURNA (voretigene neparvovec-rzyl)" (PDF). U.S. Food & Drug Administration. Retrieved 2019-11-25.. ... Keen, Eric C (July 2013). "Beyond phage therapy: virotherapy of protozoal diseases". Future Microbiology. 8 (7): 821-823. doi: ... "Package Insert - ZOLGENSMA" (PDF). U.S. Food & Drug Administration. Retrieved 2019-11-25.. ...
... hence blocks phage TerS/TerL complex formation responsible for phage DNA packaging. In second mechanism PICI CpmAB redirect the ... phage capsid morphogenetic protein to make 95% of SaPI-sized capsid and phage DNA can package only 1/3rd of their genome in ... In 2005, three independent research groups showed that some CRISPR spacers are derived from phage DNA and extrachromosomal DNA ... furiosus both target the mRNA of phages rather than phage DNA genome,[66][120] which may make these systems uniquely capable of ...
To clone longer lengths of DNA, lambda phage with lysogeny genes deleted, cosmids, bacterial artificial chromosomes, or yeast ... Examples of software packages that handle plasmid maps are ApE, Clone Manager, GeneConstructionKit, Geneious, Genome Compiler, ... Linear DNA has free ends, either because both strands have been cut or because the DNA was linear in vivo. This can be modeled ... Nicked open-circular DNA has one strand cut.. *Relaxed circular DNA is fully intact with both strands uncut but has been ...
2 Chemical modifications and altered DNA packaging *2.1 Base modifications and DNA packaging ... In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell ... DNA exists in many possible conformations that include A-DNA, B-DNA, and Z-DNA forms, although, only B-DNA and Z-DNA have been ... Further information: DNA supercoil. DNA can be twisted like a rope in a process called DNA supercoiling. With DNA in its " ...
Examples are methylation patterns of the DNA molecule itself and proteins involved in packaging DNA, such as histones (also ... Casadesús J, D'Ari R (2002). "Memory in bacteria and phage". BioEssays. 24 (6): 512-8. doi:10.1002/bies.10102. PMID 12111734.. ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad.947102. ... Gehring M, Henikoff S (2007). "DNA methylation dynamics in plant genomes". Biochim. Biophys. Acta. 1769 (5-6): 276-86. doi: ...
... ng phage DNA kapag ito ay pumapasok sa selulang bacterial na umaasal bilang bahagi ng sistemang restriksiyong modipikasyon. Sa ... Ang mga modipikasyon ng base ay maaaring sangkot sa pagkakahon(packaging) na ang mga rehiyon may mababa o walang ekspresyon ng ... Ang DNA ay umiiral sa maraming mga posibleng kompormasyon na kinabibilangan ng mga anyong A-DNA, B-DNA, at Z-DNA bagaman ang ... Sa replikasyon ng DNA, ang nakabatay sa DNA na DNA polymerase ay gumagawa ng kopya ng sekwensiyang DNA. Ang pagiging tiyak ay ...
... mitochondrial DNA packaging protein in Physarum polycephalum and causes intense chromatin condensation without suppressing DNA ... Human mitochondrial DNA deletions associated with mutations in the gene encoding Twinkle, a phage T7 gene 4-like protein ... Mitokondriaalsed nukleoidid on DNA-valk kompleksid, mis esinevad mitokondrites. Mitokondriaalne DNA (mtDNA) sarnaselt tuuma DNA ... The Strictly Aerobic Yeast Yarrowia lipolytica Tolerates Loss of a Mitochondrial DNA-Packaging Protein. Eukaryotic Cell 13: ...
Package delivery, search and rescue Hovertrain, Ground effect train Research, development[145][146]. Trains with higher speed ... Human DNA vaccination Clinical trials Enzybiotics Successful first trials Genetic engineering of organisms and viruses Research ... Phage therapy First trial uses Plantibody clinical trials Regenerative medicine Some laboratory trials[100]. Life extension ... Smartstores - RFID based self checkout (keeping track of all incoming and outgoing products), food packaging, smart shelves, ...
The matter was finally settled when a biology student wrote an article about the migration of greep DNA through a variety of ... "Phage Pie Euphraino U Komrad", which translated to "Eat, Drink and be Merry." [The floating "U" was originally a typographical ... reference is made to the existence of a novice package in the pages of the Sharp Zhurnals, while several of the APA's ...
The packaging of eukaryotic DNA into chromatin presents a barrier to all DNA-based processes that require recruitment of ... conserved mechanisms from phage to humans". Molecular Cell. 8 (6): 1163-74. doi:10.1016/S1097-2765(01)00419-1. PMID 11779493. ... structures of some DNA repair enzymes Human DNA repair diseases DNA repair special interest group DNA Repair DNA Damage and DNA ... Reduced expression of DNA repair genes causes deficient DNA repair. When DNA repair is deficient DNA damages remain in cells at ...
Lambda phages). A vector containing foreign DNA is termed recombinant DNA. The four major types of vectors are plasmids, viral ... However, because viral vectors frequently are lacking infectious sequences, they require helper viruses or packaging lines for ... Plasmid Viral vector Cloning vector Expression vector Hybrid vector Minicircle Recombinant DNA Naked DNA Vector (epidemiology ... An artificial chromosome can carry a much larger DNA fragment than other vectors. YACs and BACs can carry a DNA fragment up to ...
They are the virophage-specific major and minor capsid proteins (MCP and mCP), PRO (cysteine protease), and a DNA-packaging ... Virophages are small, double-stranded DNA viral phages that require the co-infection of another virus. The co-infecting viruses ... In metagenomic analysis, DNA sequences are run through multiple bioinformatic algorithms which pull out certain important ... Virophages have small double-stranded DNA genomes that are either circular or linear in shape. The size of these genomes can ...
Single step high level resistance to the rifamycins occurs as the result of a single amino acid change in the bacterial DNA ... "Drug Approval Package: Aemcolo (rifamycin)". U.S. Food and Drug Administration (FDA). 21 December 2018. Retrieved 27 December ... discovered that the cell wall lacks mycolic acid and is not able to be infected by the Nocardia and Rhodococcus phages. Based ... The antibacterial activity of rifamycins relies on the inhibition of bacterial DNA-dependent RNA synthesis. This is due to the ...
These selected phages are then subjected to DNA sequencing.[page needed] Cell surface display systems can also be utilized to ... A guide tree is then constructed using the UPGMA method that is used by the HH align package. This guide tree is used to ... Finally this method is independent of the length of DNA template sequence, and requires a small amount of parental DNA.[page ... This method involves the fusion of a 3-methyladenine DNA glycosylase to tetR DNA-binding domain. This has been shown to ...
... a protease enzyme that empties the inside of the capsid prior to DNA packaging, and a terminase enzyme that packages viral DNA ... Keen EC (January 2015). "A century of phage research: Bacteriophages and the shaping of modern biology". BioEssays. 37 (1): 6-9 ... Rao VB, Feiss M (November 2015). "Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses". Annu Rev Virol. 2 (1): 351 ... For tailed bacteriophages, after DNA packaging, the tail of the virion, which was assembled separately, is attached to the ...
Paruch L, Paruch AM, Sørheim R (March 2020). "DNA-based faecal source tracking of contaminated drinking water causing a large ... Fletcher RD (1965). "Activity and morphology of Vibrio coli phage". American Journal of Veterinary Research. 26 (111): 361-4. ... FoodNet Canada has reported that Campylobacter was the most common pathogen found on packaged chicken breast, with nearly half ...
The rate of DNA replication in living cells was first measured as the rate of phage T4 DNA elongation in phage-infected E. coli ... DNA and Chromosomes 4.1: The Structure and Function of DNA 4.2: Chromosomal DNA and Its Packaging in the Chromatin Fiber Ch 5: ... DNA packaged and condensed in this way is called chromatin. The manner in which DNA is stored on the histones, as well as ... This DNA has often been referred to as "junk DNA". However, more recent analyses suggest that, although protein-coding DNA ...
... and vector DNA that is too small cannot be properly packaged into the phage. This property can be used for selection - vector ... therefore to allow foreign DNA to be inserted into phage DNA, phage cloning vectors may need to have some non-essential genes ... The bacteriophages used for cloning are the λ phage and M13 phage. There is an upper limit on the amount of DNA that can be ... The vector and the foreign DNA may be treated with a restriction enzyme that cuts the DNA, and DNA fragments thus generated ...
... yield of packaged phage DNA per induced lysogen in the presence of the methylase relative to the yield of packaged phage DNA ... yield of packaged phage DNA per induced lysogen in the presence of the methylase relative to the yield of packaged phage DNA ... Packaged unmethylated and EcoO109I methylated phage DNA was extracted from 100-μl aliquots of each phage lysate. Five nanograms ... Increased chromosome length is proposed to slow the rate of DNA packaging during the late stages of DNA packaging, thus ...
ii) DNA packaging by 9NA-like phages.The products of replication of many double-stranded DNA phages are long concatemers of the ... package DNA by a pac site-mediated headful packaging strategy. In addition, we show that 9NA initiates DNA packaging by ... uncut DNA from the indicated phage (P22 DNA is 43.5 kbp long, lambda DNA is 48.5 kbp, and phage 244 [GenBank accession no. NC_ ... Some such phages, for example, P22, P1, SPP1, Sf6, and ES18, package DNA through processive series of headful packaging events ...
T4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized BGT with UDP-glucose and a 13mer DNA fragment ... T4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized BGT with UDP-glucose and a 13mer DNA fragment ... Software Package:. Software Name. Purpose. DENZO. data reduction. SCALEPACK. data scaling. AMoRE. phasing. ... Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex. *DOI: 10.2210/pdb1M5R/pdb ...
Software Package:. Software Name. Purpose. BUSTER. refinement. XDS. data reduction. XDS. data scaling. ... Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat. *DOI: 10.2210/pdb4ZM0/pdb ... DNA/RNA (5-D(CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3). E, G. 14. Escherichia virus P1. ... DNA/RNA (5-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*A)-3). F, H. 14. Escherichia virus P1. ...
Once the DNA is packaged, the terminase detaches from the connector and the tail replaces it to finish maturation of the virion ... The terminase is composed of two subunits (a large and a small) and the small subunit recognizes the DNA to be encaspidated. ... Plays a role in packaging a single copy of genome into the prohead. ... PF11123 DNA_Packaging_2, 1 hit. ProDomi. View protein in ProDom or Entries sharing at least one domain. PD029080 PD029080, 1 ...
Viral DNA and DNA Replication Strategies of Various dsDNA Phages (pdf file ... DNA Packaging in DS DNA Phages by ... Translocation of DNA based on connector rotation and symmetry mismatch between the connector and the DNA in SPP1. (tif ... Schematic of selected strategies for DNA maturation and packaging. (tif) Fig ...
Conserved Protein Domain Family Phage_Nu1, Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer ... Phage DNA packaging protein Nu1. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of ... subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA. ...
This phage, which we named PPSC2, has a genome that is... ... Black LW, Rao VB (2012) Structure, assembly, and DNA packaging ... We isolated a Pseudomonas phage infecting Pseudomonas fluorescensSA1 separated from a soil sample collected in Sichuan Province ... This phage, which we named PPSC2, has a genome that is composed of a 97,330-bp-long linear double-stranded DNA with 47.51% G+C ... Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC ...
In vitro packaging of a λ Dam vector containing EcoRI DNA fragments of Escherichia coli and phage P1. In: Gene. 1977 ; Vol. 1, ... In vitro packaging of a λ Dam vector containing EcoRI DNA fragments of Escherichia coli and phage P1. / Sternberg, Nat; ... title = "In vitro packaging of a λ Dam vector containing EcoRI DNA fragments of Escherichia coli and phage P1", ... T1 - In vitro packaging of a λ Dam vector containing EcoRI DNA fragments of Escherichia coli and phage P1 ...
Participates also in T7 DNA packaging, host DNA degradation and phage genetic recombination. ... Plays an essential role in phage DNA replication by participating in the removal of DNA-linked RNA primers. ... Yersinia phage R. Yersinia phage YpP-Y. Yersinia phage phiA1122. Yersinia phage YpP-R. Yersinia phage Y. Yersinia phage YpsP-G ... Enterobacteria phage T7M. Enterobacteria phage 3/7. Yersinia phage YpsP-G. Escherichia phage CICC 80001. Salmonella phage Vi06 ...
Phage Propagation and Preparation of Phage DNA. Isolation and propagation of phages, preparation of phage genomic DNA, and ... Phage ORF Prediction and Analysis. ORFs were predicted by using a customized in-house software package. Briefly, the primary ... Part of the DNA-replication module of phage 47 is more homologous to the corresponding region of phages ROSA, 77, 53, and 85, ... Mosaicism in S. aureus phages. (A) A highly mosaic segment of one of the DNA-replication modules of phages G1 and K. Related ...
P1 packages DNA by the "headful packaging" mechanism (20, 23). The DNA packaging of concatemeric DNA consisting of repeating ... DNA translocation, and DNA cleavage during packaging of DNA from the concatemer. Phage EC10 had a higher similarity to the ... Like a variety of other phages (e.g., P1, P22, and T7), phage T4 packages DNA by a headful packaging mechanism in which the ... Although the phage P1 terminase recognizes a specific pac sequence present in the DNA substrate, packaging of plasmid DNA that ...
The two-phage genomes shared between 60 and 70% nucleotide sequence identity over the DNA packaging, head and tail genes. ... The mutated phage replication gene was closely related to a virulence marker identified in recently emerged M3 serotype S. ... In these prophage remnants only 13-0.3 kb of putative prophage DNA was detected. We discuss the genomics data from S. pyogenes ... The superantigens are encoded between the phage lysin and the right attachment site of the prophage genome. The genes were ...
... processing and packaging of T7 DNA; and structure and assembly of phage particles. Determination of the complete nucleotide ... Gene 0.3 of bacteriophage T7 acts to overcome the DNA restriction system of the host.. J Mol Biol., 94:283-295 (1975). PubMed ... Analysis of restriction fragments of T7 DNA and determination of molecular weights by electrophoresis in neutral and alkaline ... Model for how type I restriction enzymes select cleavage sites in DNA.. Proc Natl Acad Sci USA, 85:4677-4681 (1988). PubMed ...
The insert DNA is replicated with the viral DNA; thus, together they are packaged into viral particles. These particles are ... Phage λ is a double-stranded DNA virus that infects E. coli. The λ chromosome is 48.5kb long and can carry inserts up to 25kb. ... They begin as linear DNA molecules packaged into bacteriophage P1 particles. These particles are injected into an E. coli ... The DNA is stored in a population of identical vectors, each containing a different insert of DNA. In order to construct a ...
Pruss, G; Goldstein, RN; Calendar, R (June 1974). "In vitro packaging of satellite phage P4 DNA". Proceedings of the National ... The P4 virion has a tail and an icosahedral head containing a linear double-stranded DNA genome of 11,627 kb. Phage P4 infects ... Enterobacteria phage P4 (also known as satellite phage P4) is a temperate bacteriophage strain of species Escherichia virus P2 ... It is a satellite virus which cannot engage in lytic growth without the presence of a P2-related helper phage. It generally ...
Catalano, C. E.; Cue, D.; Feiss, M. (1995). "Virus DNA packaging: the strategy used by phage λ". Molecular Microbiology. 16 (6 ... Production and assembly of stable proheads is an essential precursor to bacteriophage genome packaging; this packaging activity ... as seen with the prohead of Bacillus subtilis phage φ29. ...
Visualisation of phage virions by transmission electron microscopy established that this phage belongs to the family ... Visualisation of phage virions by transmission electron microscopy established that this phage belongs to the family ... To understand the interactions between these organisms and the phages that infect them, a number of phages were isolated ... a number of phages were isolated against lactococcal strains of non-dairy origin. One such phage, ФL47, was isolated from a ...
DNA packaging of phages phi29, T3 and T7 sometimes produces incompletely packaged DNA with quantized lengths, based on gel ... and DNA-sequencing-based phage assembly genetics. • We purify stable, mutant phage heads with a partially leaked mature DNA ... We discover here a packaging ATPase-free, in vitro model for packaged DNA length quantization. We use directed evolution to ... six sharp bands of DNA missing 3.7-12.3% of the last end packaged. Native gel electrophoresis confirms quantized DNA expulsion ...
A comparison of DNA packaging in the virions of fd, Xf, and Pf1. In: The Singe-Stranded DNA Phages. Cold Spring Harbor: Cold ... Total (phage + bacterial) DNA mass recovered as determined by Qubit (a), recovered phage:cell ratio (b) and DNA composition by ... Recovery and mass yield from mock skin and swab samples with phage T4. Bacterial (a) and phage T4 (b) DNA recoveries were ... 2c), corresponding to a 67-fold increase, on average, in the proportion of phage DNA out of total DNA, compared to the ...
2008) The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 135:1251- ... 1985) DNA packaging of bacteriophage T4 proheads in vitro. Evidence that prohead expansion is not coupled to DNA packaging. J ... The genomic DNA is then packaged into the empty prohead through the portal vertex by an ATP-driven packaging motor containing ... 2015) Mechanisms of DNA packaging by large double-stranded DNA viruses. Annu Rev Virol 2:351-378. ...
Several phages that infect Vibrio coralliilyticus, a widespread coral pathogen, have been isolated, suggesting that this ... This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy ... This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy ... coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic ...
The researchers used fluorescently labeled phage DNA to investigate in...,Basis,for,DNA,ejection,from,single,phage,particles, ... Almost all phages (also known as bacteriophages) are formed of a capsi...Phage nucleic acid transport poses a fascinating ... Studying phage a primitive class of virus that infects bacteria by in... ... It was hypothesized that the internal pressure built during packaging of the DNA in the phage capsid was responsible for DNA ...
Study DNA Chemistry and Analysis flashcards from Adam Purviance ... a large amount of DNA can be packaged into a small area ... lambda phage 62 _____ are plasmids which contain DNA sequences that allow DNA to be packaged into a bacteriophage protein coat ... The H1 histone, though binding to both the DNA of the ____ particle and the ___ DNA, plays an important role in packaging while ... DNA molecules are created by linking restriction fragments of DNA from one organism with another. Generally the DNA fragments ...
Ligated DNA was packaged into phage using Gigapack packaging extract (Stratagene) according to manufacturers instructions. The ... Estimates of such homology are provided by either DNA-DNA or DNA-RNA hybridization under conditions of stringency as is well ... The resultant double-stranded DNA was methylated by DNA methylase (Promega) prior to filling-in its ends with T4 DNA polymerase ... Phage DNA was purified from the culture as described in Sambrook et al. (Molecular Cloning, A Laboratory Manual, 2nd ed. (1989 ...
As mentioned above, P1 packages ~90 kb of DNA. This means that genes in the vicinity of your target gene in the recipient will ... Most of the bacteria are lysed by phage that packaged P1 genomes, but a fraction of the phage inject a genome segment derived ... Today, phage P1 is commonly used as a transducing agent because it is a generalized tranducer (it can package random sections ... As mentioned above, P1 packages ~90 kb of DNA. This means that genes in the vicinity of your target gene in the recipient will ...
... contain single-stranded circular DNA of about 6400 bases (1). They penetrate the host cell via pili induced by the F-episome of ... Filamentous phages are quite flexible on the size of the DNA to be packaged. They spontaneously generate miniphages of about 1 ... if the phage packaging signal is provided (4).. Keywords. Replication Origin Phage Particle Complementary Strand Filamentous ... Schaller, H., Beck, E. and Takanami, M. (1978) in: "The Single-Stranded DNA phages" Cold Spring Harbor Laboratory, Cold Spring ...
... and DNA packaging, p. 103-157. In N. Symonds, A. Toussaint, P. van de Putte, and M. M. Howe (ed.), Phage mu. Cold Spring Harbor ... Preparation and sequencing of phage genomic DNA.Initially, DNA sequence was obtained from restriction fragments of the phage ... When necessary, sequence was determined directly from phage genomic DNA, which was prepared as outlined for phage λ and ... and phage purification and DNA extraction were performed as described for phage λ (43). Luria-Bertani broth and agar (43) were ...
Using the purified phi29 components, in vitro DNA packaging and phage assembly was performed as described previously.[51] Phage ... Motor Function in Packaging of DNA. 2.2.1. Function of EGFP-gp16 in Driving the Motor for DNA Packaging A DNA packaging assay ... that overstretches the DNA.[40] The plot of DNA tether length versus packaging time shows that the DNA packaging process ... B) Temporal micrographs of a tethered bead showing the phi29 DNA packaging behavior. C) DNA tether length against packaging ...
When a new "phage" is assembled within a host cell, it is faced with a difficulty-how to package its DNA, which is 1,000 times ... Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proceedings of the ... The Structure of the Phage T4 DNA Packaging Motor Suggests a Mechanism Dependent on Electrostatic Forces. Cell. 135 (7): 1251- ... The December 26, 2008, edition of the journal Cell reported on the nuts and bolts of the viral DNA packaging motor.4 It ...
  • These phages, along with Salmonella phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly related Proteus phage PmiS-Isfahan, have similarly sized genomes of between 52 and 57 kbp in length that are largely syntenic. (
  • Their genomes also show substantial genome mosaicism relative to one another, which is common within tailed phage clusters. (
  • Their core genomes are much more closely related to one another than to the genome of any other known phage, and they comprise a well-defined cluster within the family Siphoviridae . (
  • This work describes the genomes of three new 9NA-like phages and the results of experimental analysis of the proteome of the 9NA virion and DNA packaging into the 9NA phage head. (
  • These phage genomes offer an exciting opportunity to discern molecular mechanisms of phage evolution and diversity. (
  • Recent sequence analyses of bacteriophages from Mycobacterium tuberculosis and other bacterial species indicates that between 50% and 75% of ORFs predicted from the phage genomes have no match in GenBank ( 4 - 6 ). (
  • The two-phage genomes shared between 60 and 70% nucleotide sequence identity over the DNA packaging, head and tail genes. (
  • Recent nucleotide and whole-genome analyses have revealed that most bacterial genomes contain large amounts of bacteriophage DNA ( 18 ). (
  • This suggests that lateral gene transfer contributes to the genetic diversity of bacterial genomes ( 2 ), and we hypothesized that DNA fragments are transferred among bacteria at higher rates than those shown by culture-based methods using selective media. (
  • Phage capsids are extremely stable and able to sustain high internal pressure exerted by their tightly packed genomes ( 3 , 4 ). (
  • Most of the bacteria are lysed by phage that packaged P1 genomes, but a fraction of the phage inject a genome segment derived from the donor host. (
  • The genetic organization of the serotype conversion and integration-excision modules is highly conserved among the genomes of the glucosylating phages (reviewed in reference 4 ), and this organization is also conserved in Salmonella enterica serovar Typhimurium serotype-converting phage P22 ( 48 ). (
  • But we're short of genies and so far in vivo measurement of these kinetics has not been made (except for the stubby-tailed phage T7 and kin that transfer their genomes by an entirely different and significantly slower mechanism…a story for a future post). (
  • Mechanics models can't explain the transfer of single-stranded RNA or DNA phage genomes that are packaged at much lower density and thought to not be under pressure. (
  • The Siphoviridae genomes are usually organized into six functional modules: lysogeny, DNA replication, regulation of transcription, packaging and head, tail, and lysis ( 4 ). (
  • It is indicative in this respect that several sequenced genomes of these bacteria possess large extrachromosomal elements encoding plasmid-related and phage-related functions [ 1 , 5 , 8 - 12 ]. (
  • ssDNA genomes to package into viruses are created from this by a rolling circle mechanism. (
  • During HSV-1 replication, viral DNA is synthesized in the infected cell nucleus, where a large, branched concatemer consisting of many genomes is formed ( 15 , 21 , 34 , 54 ). (
  • UL89 cleaves the long DNA concatemers into unit-length genomes of appropriate length for encapsidation. (
  • Lactococcus lactis phage BK5-T and Streptococcus thermophilus phage Sfi21, two cos-site temperate Siphoviridae with 40-kb genomes, share an identical genome organization, sequence similarity at the amino acid level over about half of their genomes, and nucleotide sequence identity of 60% over the DNA packaging and head morphogenesis modules. (
  • Beginning in the mid‐twentieth century, studies focused on bacteriophage T4 revealed essential features of the molecular nature of genes and genomes, mechanism and fidelity of DNA replication, genetic recombination, DNA repair, control of gene expression, genome organisation, assembly of complex macromolecular structures and pre‐emption of cell metabolism by virus infection. (
  • We present here the complete genomes of 18 phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. (
  • A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3,738 apparently complete phage genomes that represent 451 putative genera. (
  • Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. (
  • Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. (
  • Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. (
  • The VCU portion of the study was led by Gail Christie , Ph.D., professor of microbiology and immunology in the VCU School of Medicine, who has spent more than 30 years studying the interactions between bacterial viruses, or phages, and bacterial genomes to gain a better understanding of how disease can spread on the molecular level. (
  • According to Christie, bacterial genomes are constantly changing due to the acquisition of new DNA that can bring in new traits. (
  • Understanding these mechanisms will allow the identification of targets for blocking not only the spread of SaPIs, but of the helper phages themselves - many of which carry additional toxin genes on their own genomes," said Christie. (
  • According to Christie, this is particularly important because clinical isolates of S. aureus carry both SaPIs and potential helper phages in their genomes, and the replication and spread of these elements can be induced by antibiotic treatment. (
  • In British patent application no. 8525252 (publication no. 2166445) there are described various DNA sequences which may be used as probes to hybridize individually at a number of polymorphic sites within the human and animal genomes enabling the production of a "fingerprint" composed of marked bands of differing molecular weights. (
  • On rare occasions, bits of bacterial DNA get packaged in the phage capsules instead and get added to the genomes of subsequently infected bacteria. (
  • Genomes are linear, double stranded DNA, and are relatively small (between 16-20 kbp)-hence the term pico-virinae. (
  • Picoviruses package linear, monomeric genomes with a terminal protein covalently attached to each end. (
  • Using this strategy, we have previously shown that several Staphylococcus aureus bacteriophages encode proteins that target components of the DNA replication and RNA transcription machinery ( 12 ). (
  • Almost all phages (also known as bacteriophages) are formed of a capsi. (
  • Almost all phages (also known as bacteriophages) are formed of a capsid structure, or head, in which the viral genome is packaged during morphogenesis, and a tail structure that ensures the attachment of the phage to the host bacteria. (
  • Filamentous bacteriophages (fd, M13, f1) contain single-stranded circular DNA of about 6400 bases (1). (
  • By linking the phage content to dominant S. aureus clonal complexes we could show that the distribution of bacteriophages varied remarkably between lineages, indicating restriction-based barriers. (
  • In its dimensions and oligomeric state, the pUL6 portal resembles the connector or portal complexes employed for DNA encapsidation in double-stranded DNA bacteriophages such as φ29, T4, and P22. (
  • In its basic features, HSV-1 DNA encapsidation resembles that observed in double-stranded DNA (dsDNA) bacteriophages, such as P22, T7, and λ. (
  • Bacteriophage assembly proceeds through the formation of spherical precursor capsids (procapsids), and bacteriophages have a unique vertex, a dodecameric ring of 12 proteins, through which the DNA enters and exits the capsid ( 3 , 45 ). (
  • Bacteriophages, or "phages" as they are commonly known, were allowed only as a last resort in cases like Patterson's. (
  • We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. (
  • To begin to understand how CPSs have an impact on Bacteroides-phage interactions, we isolated 71 Bacteroides thetaiotaomicron-infecting bacteriophages from two locations in the United States. (
  • Our emerging view of the gut microbiome largely focuses on bacteria, while less is known about other microbial components, such as bacteriophages (phages). (
  • Since bacteriophages are extremely common among bacteria-a drop of seawater contains millions of bacteriophages, for example-other combinations of disease-causing species could engage in phage-mediated toxin gene transfer. (
  • The high frequency of genetic transfer suggested that other bits of DNA could be passed along, and the scientists showed in another experiment that staphylococcal plasmids containing antibiotic resistance genes could also be transferred to Listeria via bacteriophages. (
  • Bacteriophages (phages) are probably the most abundant entities in nature, often exceeding bacterial densities by an order of magnitude. (
  • Assembly and maturation of double-stranded DNA bacteriophages. (
  • In phage therapies, CRISPR-wielding bacteriophages may kill bacteria or compel them to carry out useful functions. (
  • Bacteriophages, called phages for short, were discovered independently by Frederick Twort in 1915 and Félix d'Herelle in 1917, over a decade before penicillin, the most well known antibiotic. (
  • The following genera are recognized: Cepunavirus (formerly Cp1virus, with species Streptococcus virus Cp1 aka Complutense phage 1, Cp-1) Negarvirus Salasvirus The following species are unassigned to a genus: Actinomyces virus Av1 Mycoplasma virus P1 Two bacteriophages in this family have been found to infect and lyse Clostridium perfringens. (
  • Native gel electrophoresis confirms quantized DNA expulsion and, after removal of external DNA, provides evidence that capsid radius is the quantization-ruler. (
  • Capsid-based DNA length quantization possibly evolved via selection for stalling that provides time for feedback control during DNA packaging and injection. (
  • Thus, we hypothesize leaked DNA quantization via variably quantized capsid radius. (
  • The structure of a T=13 icosahedral head assembly, in which the major capsid protein of T4 phage had a single mutation at a residue in the interface between neighboring subunits, has been determined to 3.3-Å resolution. (
  • A common feature of phages is that during infection, only their genome is transferred to the bacterial host's cytoplasm, whereas the capsid and tail remain bound to the cell surface. (
  • It was hypothesized that the internal pressure built during packaging of the DNA in the phage capsid was responsible for DNA ejection. (
  • A classic dark field image of the DNA molecule released by rupture of a single T4 capsid. (
  • A popular answer invokes the pressure inside the phage capsid, and that pressure is not negligible. (
  • The DNA within a T4 virion is estimated from indirect measurements to exert a pressure on the capsid of about 60 Atm, the result of being packaged at very high density (on the order of 500 mg ml -1 ) and confined in tight quarters against its will. (
  • The double-stranded DNA (dsDNA) of phage T4, for example, is about 50 μm long, whereas its capsid diameter is only about 1/1000 of that (85 nm). (
  • Tightly coiled inside the capsid, the DNA double helix pushes back due to its inherent bending resistance and the mutual repulsion of its negatively-charged phosphate backbone. (
  • Stuffing all the DNA into the capsid in the first place, against ever-increasing resistance takes work. (
  • The DNA 'packaging motor' of phage φ29 can move its DNA into a capsid against a force of at least 100 pN (whereas molecular motors such as dynein and kinesin exert a force of only 5-7 pN). (
  • A major one is that as more and more of the DNA passes into the cell, the pressure within the capsid drops. (
  • The resulting DNA-filled capsid is subsequently converted into an infectious virion. (
  • When a new "phage" is assembled within a host cell, it is faced with a difficulty-how to package its DNA, which is 1,000 times longer than the diameter of its capsid, the tiny vessel that holds it. (
  • Each protein takes its turn, running counterclockwise, to shove two DNA bases at a time into its capsid. (
  • Here we report the results of experiments carried out to test the idea that the HSV-1 UL6 gene product (pUL6) forms the portal through which viral DNA passes as it enters the capsid. (
  • The results are interpreted to support the view that pUL6 forms the DNA entry portal, since it exists at a unique site in the capsid and forms a channel through which DNA can pass. (
  • The virus DNA is contained inside the capsid. (
  • Packaging is considered to begin with the procapsid, a spherical intermediate in assembly of the mature capsid ( 27 , 36 ). (
  • When cells are infected with HSV-1 mutants lacking the function of any of the seven genes, capsid formation and DNA replication occur normally, but no packaging takes place. (
  • The portal vertex is the docking site for the packaging proteins, such as terminase, the protein responsible for cleavage of monomeric units from concatemeric DNA and translocation of DNA into the capsid in an ATP-dependent fashion ( 5 , 7 , 8 , 45 ). (
  • The fluorescent phage is a "hybrid", co-expressing wild- type and YFP-fusion versions of the capsid gpD protein. (
  • In a first project, the dynamics of the DNA ejection through the tight viral shaft from the highly packed phage capsid was investigated. (
  • During phage assembly the phage DNA is very tightly packaged into the phage capsid. (
  • The question arises if the internal pressure resulting from the high DNA density inside the capsid is responsible for the complete or at least the partial DNA transfer into the host during infection. (
  • In the assembly of many phages a hollow protein capsid assembles first and is then filled with DNA by the action of a tiny "molecular motor" which is powered by chemical energy (ATP hydrolysis). (
  • We use optical tweezers to pull on a single DNA molecule as it is being packaged into a single phage capsid. (
  • This suggested that, in the presence of the SaPI, a portion of the pool of capsid proteins assembles into smaller capsids which are then filled with SaPI DNA. (
  • It results in extremely high transfer frequencies, reduces the number of ORFs the SaPI has to carry around, and ensures that the SaPI replicates only when there is a suitable phage present, ready to provide it with capsid proteins. (
  • All herpesviruses contain a linear double-stranded DNA genome, enclosed within an icosahedral capsid. (
  • All herpesviruses have a portal pore for capsid assembly and DNA packaging and ejection. (
  • In addition, they interact with the terminase complex, which provides the energy and force necessary for packaging the DNA inside the capsid and cleaves the DNA at the appropriate site. (
  • The HBV virion consists of a DNA genome enclosed within an icosahedral capsid, in turn enclosed within a lipoprotein envelope. (
  • and the structure of the Primary Enveloped Virion - the particle produced when the mature, DNA-filled capsid buds out of the nucleus where it assembles into the perinuclear space. (
  • Once the capsid is packaged with the DNA, the terminase complex is substituted by the connector proteins gp15. (
  • By an unknown mechanism, DNA moves from the compartment into the capsid. (
  • As a T4 virus assembles itself, the lower ring of the motor structure attaches to a strand of DNA, while the upper ring attaches to a capsid. (
  • The process draws the DNA strand upwards into the capsid where it is protected from damage, enabling the virus to survive and reproduce. (
  • After the DNA is inside the capsid, the motor falls off, and a virus tail attaches to the capsid. (
  • Previous work, by this team with additional collaborators, has focused on one aspect of this interference - the ability of the SaPIs to change the size of the capsid, or head, of the helper phage so that the smaller SaPI genome can be packaged but a complete helper phage genome cannot. (
  • An electron micrograph that illustrates the two different viral particles - the helper phage is the one with the larger capsid, and the SaPI-containing one with the smaller capsid. (
  • On infection, the RNA can be directly translated into proteins that replicate the phage RNA and direct the synthesis of any capsid proteins required to form new phage particles. (
  • MANY double-stranded DNA viruses have replication and recombination pathways that produce concatemers, i.e. , end-to-end multimers of virus chromosomes. (
  • This phage, which we named PPSC2, has a genome that is composed of a 97,330-bp-long linear double-stranded DNA with 47.51% G+C content and 168 putative protein-coding genes. (
  • The P4 virion has a tail and an icosahedral head containing a linear double-stranded DNA genome of 11,627 kb. (
  • The challenges and outcomes of this basic research spurred the development of some widely used research methods, including sedimentation to measure size and shape of single- and double-stranded DNA, and slab gels for electrophoresis of proteins and nucleic acids. (
  • During the penetration process their single-stranded genome is converted into double-stranded DNA which is the main viral component in the first minutes after infection. (
  • PRD1 is an icosahedral double-stranded (ds)DNA bacterial virus with an internal membrane. (
  • 4 , 26 ] It was found that gp16 binds the 5′/3′ helical double-stranded end of pRNA during DNA packaging[ 27 ] and the binding to pRNA enhances the ATPase activity of gp16. (
  • This is the mechanism by which the double stranded supercoiled genome is nicked on the positive strand by a virus-encoded A protein, also attracting a bacterial DNA polymerase (DNAP) to the site of cleavage. (
  • This similarity supports the proposed evolutionary relationship between herpesviruses and double-stranded DNA phages and suggests the basic mechanism of DNA packaging is conserved. (
  • Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. (
  • Bacteriophage T4 contains a large, linear double‐stranded DNA genome, with chemical modifications of its cytosine residues. (
  • Refers to an end of a double stranded-DNA molecule, which has neither a protruding 5' nor 3' strand end. (
  • In a double-stranded DNA molecule the bases of matching nucleotides pair with one another by hydrogen bonding. (
  • The phage TW1 genome consists of 39,940-bp-length double-stranded DNA with a GC content of 40.19 %, and it was predicted to have 62 open reading frames (ORFs), which were classified into functional groups, including phage structure, packaging, DNA metabolism, regulation, and additional function. (
  • Genome of phage PHS3 consisted of a linear, double-stranded 35.626 kb DNA molecule with 40.85% GC content, and 58 putative open reading frames (ORFs) without tRNA. (
  • To begin to characterize this group of phages in more experimental detail, we identified the genes that encode the major virion proteins and examined the DNA packaging of the prototypic member, phage 9NA. (
  • Comparative nucleotide and protein sequence analysis indicates that these phages are a remarkable source of untapped genetic diversity, encoding 2,170 predicted protein-encoding ORFs, of which 1,402 cannot be annotated for structure or function, and 522 are proteins with no similarity to other phage or bacterial sequences. (
  • Determination of the complete nucleotide sequence of T7 DNA , 39,937 base pairs, revealed coding sequences for more than fifty T7 proteins and the arrangement of signals that direct gene expression. (
  • The grooves in the DNA provide surfaces to which regulatory proteins can bind. (
  • Geider K., Meyer T.F., Bäumel I., Reimann A. (1984) Proteins and Nucleotide Sequences Involved in DNA Replication of Filamentous Bacteriophage. (
  • These ORFs are transcribed in the opposite orientation to the serotype conversion genes, and the protein encoded by orf-3 shows homology to other phage tail fiber assembly proteins ( 27 ). (
  • Nor can they explain the transfer of phage internal proteins…and all phages transfer at least some . (
  • At a minimum, tail plug proteins have to go, and for the long-tailed phages, there is also a tape measure protein that has to get out of the way before the DNA can exit via the tail tube. (
  • Some phages package essential proteins in the virion, proteins needed in the cell immediately in order to get past host defenses and/or initiate replication. (
  • We also report a DNA translocation machinery composed of at least three viral integral membrane proteins, P14, P18 and P32. (
  • 4 It consists of five proteins in a ring that wraps around the DNA strand. (
  • Each of the five proteins goes through a sequence of events: binding ATP (enabled by the exact placement of a specific amino acid, arginine), binding the DNA, cranking the DNA upward, then releasing and resetting. (
  • This bacteriophage has a [+] circular single-stranded DNA genome of 5386 nucleotides encoding 11 proteins . (
  • As it translocates around the genome it displaces the outer strand of already-synthesised DNA, which is immediately coated by SSBP proteins. (
  • Studies to clarify the mechanism of HSV-1 DNA encapsidation have focused on specific, conserved, cis -acting DNA sequences (pac sites) ( 23 , 38 , 40 , 49 ) and on trans -acting, virus-encoded proteins. (
  • Genetic analyses have identified a total of seven HSV-1-encoded proteins, products of the genes UL6, UL15, UL17, UL25, UL28, UL32, and UL33, that are demonstrated to be specifically involved in DNA packaging ( 14 , 51 ). (
  • Mass spectrometry and N-terminal sequencing showed nine Xop411 coat proteins, among which three were identified, six were assigned as coat proteins (4) and conserved phage proteins (2) in Xp10. (
  • The structural genes from BK5-T shared no sequence relationships with corresponding genes/proteins from lactococcal phages belonging to distinct lactococcal phage species, including phage sk1 (phage species 936) that showed a closely related gene map. (
  • Despite a clearly distinct genome organization, lactococcal phages sk1 and c2 showed nine sequence-related proteins. (
  • The elongated icosahedral head (in grey) contains four exterior proteins and within its interior, DNA and six different proteins. (
  • A type of electrophoresis gel made up of polyacrylamide used for resolving proteins (as in SDS-PAGE) and shorter DNA molecules in native electrophoresis. (
  • M13 wraps up strands of DNA (programmed by scientists) and sends them out in proteins that infect cells and release the DNA messages once they have gained entry. (
  • The proteins in those particles were all phage-encoded, including all of the phage structural proteins. (
  • Antibodies are the first proteins which were successfully displayed on the surface of phage by fusing the coding sequence of scFv or Fab to the coat protein. (
  • In addition to viral DNA, certain proteins gain entry into this compartment, including viral proteins involved in DNA and mRNA synthesis, and at least one host cell protein. (
  • Phage SPP1 can attach to membrane vesicles released by susceptible strains of B. subtilis , showing that they contain viral receptor proteins. (
  • However, genes related to lysogeny and host lysis were not detected in the phage TW1 genome, indicating that annotation information about P. phenolica phages in the genome databases may not be sufficient for the functional prediction of their encoded proteins. (
  • Thanks to Sidhu adaptations, he found a way to use a phage display - which was first developed in the '80s for studying proteins - to produce antibodies faster and on an unprecedented scale. (
  • Prokaryotic DNA lacks histones (packaging proteins ), although other packaging proteins are present, and molecules have easier access to DNA compared with eukaryotes. (
  • Their gene content ranges from 80 to 99 predicted genes, of which 40 are common to all seven and form the core genome, which includes all identifiable virion assembly and DNA replication genes. (
  • Viral DNA and DNA Replication Strategies of Various dsDNA Phages (pdf file). (
  • Plays an essential role in phage DNA replication by participating in the removal of DNA-linked RNA primers. (
  • The mutated phage replication gene was closely related to a virulence marker identified in recently emerged M3 serotype S. pyogenes strains in Japan. (
  • P1 vir is a mutant phage that enters the lytic cycle upon infection (ensuring replication and lysis). (
  • During the replication and lysis of the phage in a culture of bacteria, a small percentage of the phage particles will contain a genome segment that contains your gene of interest. (
  • Once inside the host bacterium, replication of the [+] ssDNA genome proceeds via negative sense DNA]] intermediate. (
  • During replication of herpes simplex virus type 1 (HSV-1), viral DNA is synthesized in the infected cell nucleus, where DNA-free capsids are also assembled. (
  • During viral replication, herpesviruses package their DNA into the procapsid by means of the terminase protein complex. (
  • During phage replication, bacterial DNA can be packaged into a small proportion of phage particles either instead of or as well as the phage genome. (
  • zebrafish and mice, bacteriophage T4 still presents the best opportunities for understanding at the molecular level DNA replication and recombination, and macromolecular assembly. (
  • these features protect against information loss during replication of a linear DNA. (
  • The T4 genome encodes numerous enzymes, used to support replication of the viral genome and to synthesise deoxyribonucleotides to support the enormous rate of DNA accumulation in infected cells. (
  • Generation of a population of linear DNA molecules that are circularly permuted and terminally redundant with respect to base sequence, by cutting of a concatemeric replication intermediate. (
  • In mice, aging is accompanied by changes in expression of genes associated with increased inflammation, cellular stress, fibrosis, altered capacity for apoptosis, xenobiotic metabolism, normal cell-cycle control, and DNA replication [ 5 ]. (
  • Transcription of the viral genes, together with extensive replication of long concatameric DNA, takes place once a lytic infection is triggered. (
  • Surprisingly, a nucleus-like structure that forms during viral infection of bacteria is the site of viral DNA replication ( link to paper ). (
  • During infection of Pseudomonas bacteria with the phage 2O1phi2-1, a separate compartment forms in which viral DNA replication takes place. (
  • To lysogenize, there needs to be a DNA phase to the replication cycle and there isn't any such phase for MS2. (
  • They had a synteny in the structure and DNA replication/regulation module and shared many structural and replicate genes, while little similarity was found in the phage packaging module. (
  • Replication follows the DNA strand displacement model. (
  • They also use a typical protein primed DNA polymerase for replication, a property shared with the family Tectiviridae. (
  • Comparison of their gene maps reveals extensive genome mosaicism, hinting to a large reservoir of unidentified S. aureus phage genes. (
  • The latter point makes them attractive tools to discover and validate essential bacterial genes targeted during the phage replicative cycle. (
  • Over part of the structural genes, the similarity between SF370.2 and S. thermophilus phage O1205 extended to the nucleotide sequence level. (
  • The genes were nearly sequence identical with a DNA segment in S. equi, suggesting horizontal gene transfer. (
  • Other features that distinguish ΦL47 from Φ949 and other lactococcal phages, in addition to the presence of the tail fiber and the genome length, include a low GC content (32.5%) and a high number of predicted tRNA genes (8). (
  • P1 packages approximately 90 kb of DNA, so you can transduce genes that are linked to a selectable marker. (
  • The tail assembly and structural genes of SfV show homology to those of phage Mu and Mu-like prophages in the genome of Escherichia coli O157:H7 and Haemophilus influenzae . (
  • Similar to the other glucosylating phages, the serotype conversion genes are located immediately downstream of the attP site, which is preceded by the int and xis genes ( 26 , 27 ). (
  • Today, the temperate phages in clinical S. aureus isolates can by identified with a multiplex PCR strategy, which is based on sequence differences between viral genes coding for the surface-exposed determinants ( 28 ). (
  • In general, the evolution of phage lineages seems to be driven by the lateral gene transfer of interchangeable genetic elements (modules), which consist of functionally related genes. (
  • The pathogen evolution can thus be regarded as a constant dynamic exchange of genes between plasmids and temperate phages integrated or not into the bacterial chromosome. (
  • Still no evidence exists for the association between phages and toxicity genes in the B. cereus group, although the presence in plasmids of genes for highly effective toxins, like that of anthrax, entomotoxic crystal protein, or emetic toxin, was well documented [ 4 - 6 , 11 , 15 ]. (
  • Utilizamos diversas técnicas de biología molecular y estructural, con especial énfasis en la cristalografía de rayos X. Nuestras principales líneas de investigación son: control de la replicación de ADN, transferencia horizontal de genes, empaquetamiento del ADN en los virus, regulación de la transcripción y maquinaria de replicación viral. (
  • Gene Transfer Agents (GTAs) are related to phages, however all DNA in the host cell is randomly packaged and transmitted with no preference for the GTA genes at all. (
  • Indiscriminate DNA transfer is a highly unusual trait and could lead to the spread of any gene between bacteria, which is of great concern if these genes encode virulence factors or antibiotic resistance. (
  • Over the early gene cluster phage BK5-T shared nine regions of high nucleotide sequence similarity, covering at most two adjacent genes, with lactococcal phage r1t (phage species P335). (
  • Over the structural genes, the closest relatives of phage r1t were not lactococcal phages belonging to other phage species, but Siphoviridae from Mycobacteria (high-GC-content Gram-positive bacteria). (
  • Temperate phages can carry genes that affect the phenotype and behavior of their bacterial host. (
  • The chapter also reviews the gene organization of phage λ and then briefly describes the pattern of expression of these genes during lytic growth. (
  • When they modeled that phage therapy in the lab, however, the NYU researchers observed a phage-mediated transfer of pathogenic S. aureus genes to L. monocytogenes in raw milk. (
  • The unwitting selection of a phage with similar properties for mastitis therapy could abet the transfer of new toxin genes, Novick warns. (
  • Phage invasion into resistant cells could have a major impact on transfer of antibiotic resistance and virulence genes among bacteria. (
  • T7 breaks down the host cell's DNA to its nucleotides for it's own use (using an endonuclease and exonuclease coded by genes 3 and 6, respectively). (
  • We recognized that phage are essentially nucleic acids packaged by protein, and we know that genes and other elements in the genome are always encoded into DNA. (
  • RN [1] RM 7768817 RT Identification of related genes in phages phi 80 and P22 whose products are inhibitory for phage growth in Escherichia coli IHF mutants. (
  • A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. (
  • Some "Quimbyviridae" phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. (
  • Because phage infection can lead to transfer of host DNA from one cell to another, the results have implications for the movement of genes for antibiotic resistance or virulence. (
  • Subcloning of the mannose-resistant fimbrial genes revealed that the genetic determinants were encoded by a 6.9-kilobase-pair DNA fragment of a recombinant plasmid. (
  • However, mitoTALENs are dimeric and relatively large, making it difficult to package their coding genes into viral vectors, limiting their clinical application. (
  • Genes that grant bacteria the ability to cause disease are often found on acquired pieces of DNA known as pathogenicity islands. (
  • Molecular cloning is when genes or other DNA sequence are isolated and inserted into plasmid vectors. (
  • After a genomic library is constructed with a viral vector, such as lambda phage, the titer of the library can be determined. (
  • Several phages that infect Vibrio coralliilyticus , a widespread coral pathogen, have been isolated, suggesting that this bacterium is permissive to viral infection and is, therefore, a suitable candidate for treatment by phage therapy. (
  • Studying phage, a primitive class of virus that infects bacteria by injecting its genomic DNA into host cells, researchers have gained insight into the driving force behind this poorly understood injection process, which has been proposed in the past to occur through the release of pressure accumulated within the viral particle itself. (
  • Viral DNA delivery mechanisms offer an opportunity to obtain useful information in systems in which the process can be arrested to a number of stages. (
  • The viral protein P11 is shown to function as the first DNA delivery protein needed to penetrate the OM. (
  • The December 26, 2008, edition of the journal Cell reported on the nuts and bolts of the viral DNA packaging motor. (
  • 5 In the 60 years since this statement was made, biological magnets, wheels, and motors-including the viral DNA packing motor-have been described in considerable detail. (
  • According to Joshua Weitz, a Georgia Tech professor, he states, "In the case of perhaps the most extensively studied bacteriophage, lambda phage, experimental evidence indicates that a single infecting phage leads to host cell death and viral release, whereas if two or more phages infect a host, the outcome is typically latency. (
  • El HCMV replica su DNA en forma de concatámeros, los cuales tienen que ser cortados en genomas simples, y empaquetados dentro de la cápside viral mediante el complejo terminasa. (
  • HUMIRA is produced by recombinant DNA technology in a mammalian cell expression system and is purified by a process that includes specific viral inactivation and removal steps. (
  • As viral predators of bacteria, phages have a major impact on bacterial communities by reducing some bacteria and enabling others to flourish. (
  • Viral portal protein plays a key role in the procapsid assembly and DNA packaging. (
  • and packaging of DNA to high density by a viral motor protein, the terminase. (
  • 2007). Structural framework for DNA translocation via the viral portal protein. (
  • Packaging of the viral DNA takes place on the surface of the viral nucleus. (
  • Does infection with other phages lead to assembly of a viral nucleus? (
  • Having already determined the structures of a number of other viral components and how they self-assemble, in this study the researchers focused their attention on the small motor that some viruses use to package DNA into their 'heads', protein shells also called capsids. (
  • In this new study, the team found a second novel mechanism, which is the specific inhibition of packaging the helper phage DNA into the viral particles. (
  • When Penadés and Chen looked at the progression of phage production in S. aureus, they noticed an odd discrepancy: It seemed like the phage DNA was being replicated and packaged long before any viral DNA was being excised from the host genome. (
  • A virally encoded enzyme, terminase, carries out the cutting reaction, which is coordinated with packaging of the DNA into an empty protein shell. (
  • Based on their genome size, organization of their gene map and comparative nucleotide and protein sequence analysis, the S. aureus phages can be organized into three groups. (
  • The bacteriophage phi29 DNA packaging motor contains a protein core with a central channel comprising twelve copies of re-engineered gp10 protein geared by six copies of packaging RNA (pRNA) and a DNA packaging protein gp16 with unknown copies. (
  • Here the re-engineering of the motor DNA packaging protein gp16 by extending its length and doubling its size using a fusion protein technique is reported. (
  • This is done as the phage genome supercoils and the secondary structure formed by such supercoiling attracts a primosome protein complex. (
  • A 343-bp region of gene svp38, encoding the VSH-1 major head protein, was amplified from B. hyodysenteriae genomic DNA by PCR. (
  • A crude phage lysate is first obtained by inducing a lysogen of the gpD-EYFP (Enhanced Yellow Fluorescent Protein) phage, harboring a plasmid expressing wild type gpD. (
  • This was studied for the first time on single T5 phages whose DNA release can be triggered by the receptor protein FhuA in vitro. (
  • These phages demonstrated a gradient of relatedness ranging from nucleotide sequence similarity to protein sequence similarity to gene map similarity over the DNA packaging and head morphogenesis modules. (
  • Q binding to the cI protein will prevent the phage from undergoing a lysogenic infection. (
  • If the phage DNA is packaged into phage heads before the Int protein can function, the phage will undergo a lytic infection. (
  • If the N protein binds to the operator sites first, the phage will undergo a lysogenic infection. (
  • Scientists can send whatever they want in the DNA-everything from a sentence in a book to a sequence that encodes fluorescent protein. (
  • Members of this protein family are found in temperate phage and bacterial prophage regions. (
  • It is suggested that pRha is a phage regulatory protein. (
  • The "Gratiaviridae" phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. (
  • Given that these phage 'pro-heads' are built from just one protein and that they are pre-assembled before filling, what determines whether they will become small or large pro-heads? (
  • The detailed architecture of this protein suggests that it plays a functional role in DNA retention during packaging. (
  • Phage display is one of the most powerful and widely used laboratory technique for the study of protein-protein, protein-peptide and protein-DNA interactions. (
  • This technology is mainly based on displaying the interest protein (peptides, antibodies, scaffolds or others) on the surface of employing phage and then be used to interrogate the constructed libraries containing millions or even billions of displayed phages. (
  • Theoretically, phage display is an exogenous gene expression method which the gene encoding the interest protein is inserted into bacteriophage coat protein gene then displaying the interest protein on the phage surfaces, resulting in a connection between genotype and phenotype. (
  • A phage protein, gp105, makes up the outer layer of this compartment, which initially forms near one end of the cell, and then migrates to the center. (
  • Several phages (including SPP1, pictured) of the soil bacterium Bacillus subtilis first attach to poly-glycosylated teichoic acids (gTA), and then to the membrane protein YueB, leading to injection of DNA into the cell. (
  • It's possible that the host range of such phages could be expanded by receptor protein transfer. (
  • DNA sequence analysis of this clone revealed the identity of P37 to be FlaA, an outer sheath protein of the periplasmic flagella. (
  • How DNA is transcribed into mRNA with RNA polymerase, then translated into a protein in the ribosome with tRNA 'adaptor' molecules. (
  • Enterobacteria phage P4 (also known as satellite phage P4) is a temperate bacteriophage strain of species Escherichia virus P2 within genus Peduovirus (formerly P2-like viruses, P2virus, and P2likevirus), subfamily Peduovirinae, family Myoviridae. (
  • Phage P4 infects Escherichia coli. (
  • Sternberg, N, Tiemeier, D & Enquist, L 1977, ' In vitro packaging of a λ Dam vector containing EcoRI DNA fragments of Escherichia coli and phage P1 ', Gene , vol. 1, no. 3-4, pp. 255-280. (
  • To accurately determine the frequency of phage-mediated gene transfer, we employed cycling primed in situ amplification-fluorescent in situ hybridization (CPRINS-FISH) and investigated the movement of the ampicillin resistance gene among Escherichia coli cells mediated by phage at the single-cell level. (
  • Next, the vector DNA can be taken up by a host organism - commonly a population of Escherichia coli or yeast - with each cell containing only one vector molecule. (
  • The phi X 174 (or ΦX174 ) bacteriophage is a single-stranded DNA ( ssDNA ) virus that infects Escherichia coli , and the first DNA-based genome to be sequenced. (
  • Escherichia coli BB/1 (host for phages T3 and T7 [ 13 ]) and a Lysinibacillus are used here as Gram-negative and Gram-positive bacteria, respectively. (
  • pair fragments of human DNA in Escherichia coli using an F-factor-based vector. (
  • Chromosomal DNA from a uropathogenic strain of Escherichia coli was partially digested with the restriction enzyme EcoRI. (
  • Second, with increasing λ DNA size in the range 78 to 100% that of wild-type, the efficiency of DNA encapsidation into infectious phage particles markedly increases. (
  • and structure and assembly of phage particles. (
  • Basis for DNA ejection from single phage particles ( Studying phage a primitive class of vi. (
  • Otherwise, phage released from neighboring cells would infect and lyse the bacteria that had been infected with transducing particles. (
  • They are assembled in the host membrane into phage particles, which penetrate the cell wall without severe damage of the host. (
  • EM of phage 80α particles and a SaPI1 particle with a smaller head (arrow). (
  • They found that the infectious SaPI particles looked just like the phage particles, only smaller. (
  • Since the small particles are about 1/3 the volume of the large, and the SaPI genome is about 1/3 the size of the phage genome, it is most likely that one SaPI chromosome is packaged per particle. (
  • The partial digests were ligated into a cosmid containing an ampicillin-resistant determinant and packaged into lambda phage particles. (
  • Whole genome sequencing of ΦL47 revealed a dsDNA genome of 128, 546 bp, making it the largest sequenced lactococcal phage to date. (
  • It is an atypical dsDNA phage, as any of the vertex spikes can be used for receptor recognition. (
  • Linear dsDNA viruses translocate their genomic DNA into a preformed procapsid with remarkable speed. (
  • Bacteriophage T7 is a virulent phage with an icosahedral head, a short noncontractile tail, and a dsDNA genome of 39937 bp. (
  • A protrusion of the Phage (the tail) lengthens and attaches the Phage to the Host cell, and proceeds to send the virus' dsDNA through the channel. (
  • The total number of gene types (pangenome) in the seven phages is 176, and 59 of these are unique to individual phages. (
  • These results revealed that the difference in the number of viable cells carrying the transferred gene and the number of cells capable of growth on the selective medium was 3 to 4 orders of magnitude, indicating that phage-mediated exchange of DNA sequences among bacteria occurs with unexpectedly high frequency. (
  • Since bacteriophage-mediated gene transfer was first recognized ( 32 ), transduction has been found to occur in many phage-host systems, and various aspects of transduction, including molecular mechanisms, physiologic and genetic characterization of transductants, and ideal environments for transduction, have been investigated ( 29 ). (
  • Although these methods have led to an understanding of the genetic and physiologic characteristics of transductants and the molecular mechanism of transduction, they have limited abilities to quantify the genetic material introduced into individual cells and provide little information about gene flow among bacteria at the DNA level. (
  • This phage integrates into the thrW gene of the host, and the int attP region of SfV has been used in the development of an integrative vector that was used to construct recombinant vaccine strains ( 17 ). (
  • Seventy-one published genome sequences of staphylococcal phages were clustered into distinct integrase groups which were related to the chromosomal integration site and to the encoded virulence gene content. (
  • Additionally, phages are the primary vehicle of lateral gene transfer between S. aureus strains, providing the species with the potential for broad genetic variation. (
  • The VSH-1 svp- 38 gene was associated with a 40 kb SalI-SmaI fragment of the B. hyodysenteriae B78**T chromosome, indicating VSH-1 DNA insertion into the chromosome at a unique site. (
  • Geographical separation may have confined lateral gene transfer among the Xoo phages. (
  • Evidence for recent horizontal gene transfer between distinct phage species was obtained for dairy phages, but these transfers were limited to phages infecting the same bacterial host species. (
  • 10. The organism of claim 5 wherein the polyhydroxybutyrate polymerase gene was introduced into the organism using a vector selected from the group consisting of Agrobacterium tumefaciens plasmids and plant DNA viruses. (
  • Finally, recent analyses of DNA packaging and morphogenesis have suggested applications of T4 as a gene delivery vehicle. (
  • Phages also occasionally package host DNA and deliver it to other bacteria, in a process known as horizontal gene transfer (HGT). (
  • The researchers further posit that this mechanism enables phages to expand their host range and deliver DNA into new species, thus facilitating the attachment of phages to non-host species, providing an as-yet unexplored route for horizontal gene transfer (HGT). (
  • This aspect should be carefully considered when employing phage therapy, as phage infection of a given species may result in gene transmission into neighboring bacteria resistant to the phage," said professor Sigal Ben-Yehuda, who led the research at the Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, in the Hebrew University's Faculty of Medicine. (
  • Kunkel mutagenesis is a classic procedure for incorporating targeted mutations into a piece of DNA, so it was ideal for changing our wild-type Kumamolisin gene to code instead for specifically designed variant enzymes. (
  • Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. (
  • MRI regions are associated with unusual (non-B-form) DNA structures that are often involved in regulation of gene expression, recombination, and other genetic processes (Fedorova & Fedorov 2010). (
  • Through DNA manipulation, numerous gene variants can be created and constructed as phage display library. (
  • In order for our primers to anneal to the wild-type gene, we isolated the single stranded DNA (ssDNA) of the sense strand of our gene by growing the vector harboring our gene in a uracil-N-glycosidase (UNG) and deoxyuracil triphosphate pyrophosphatase (DUT) deficient strain of E. coli- strain CJ236. (
  • The oligo harboring the desired point mutations was then extended, using the wild-type gene and associated vector as a template, by T7 DNA polymerase. (
  • A genomic library is a collection of the total genomic DNA from a single organism. (
  • In order to construct a genomic library, the organism's DNA is extracted from cells and then digested with a restriction enzyme to cut the DNA into fragments of a specific size. (
  • Construction of a genomic library involves creating many recombinant DNA molecules. (
  • An organism's genomic DNA is extracted and then digested with a restriction enzyme. (
  • The vector containing the inserted fragments of genomic DNA can then be introduced into a host organism. (
  • In this study, we combined functional and genomic approaches to evaluate the therapeutic potential of BONAISHI, a novel V. coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). (
  • 28 , 29 ] Hydrolysis of one ATP molecule packages 2[ 4 , 25 ] or 2.5[ 30a ] base pairs of genomic DNA. (
  • Genomic islands are long stretches of chromosomal DNA that look suspiciously foreign in origin and are found in many pathogenic and non-pathogenic bacteria alike. (
  • Here, we report the complete genome sequence of a Pseudoalteromonas phage (PHS3) and major findings from the genomic analysis. (
  • Test samples of genomic DNA may be characterized by the use of polynucleotide probes each of which is specific for an informative genetic locus. (
  • It then turns to a more detailed description of a particular temperate phage λ, with an emphasis on the regulatory mechanisms that are best understood for this phage. (
  • SaPIs transfer from host to host at extremely high frequencies - provided they have some help from the right temperate phage. (
  • The phage life style prediction using PHACTS showed that it may be a temperate phage. (
  • Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. (
  • Phage infection is the single largest cause of industrial milk fermentation problems, negatively impacting on the consistency of cheese quality and resulting in large economic losses ( Coffey and Ross, 2002 ). (
  • Non-dairy lactococcal strains could potentially be exploited for use in cheese culture rotations as phage insensitive strains and may well reduce the negative consequences of phage infection within a production plant. (
  • In some cases, the titer of the phage is too high relative to the amount of bacteria in the 1:1 mix used for the transduction infection. (
  • If you put too many phage in the infection, you will kill every cell whether or not it gets a transducing particle. (
  • After tailed phages adsorb to their host and bind securely to their specific receptor on the cell surface, they inject their DNA into the cell and the infection is off and running. (
  • We could show that phages increase the genome plasticity of S. aureus during infection, facilitating the adaptation of the pathogen to various host conditions ( 11 , 12 ). (
  • Following the simultaneous infection of the cell by a number of phages, one of two pathways is chosen: lytic (virulent) or lysogenic (dormant) 3,4 . (
  • We recently developed a method for fluorescently labeling individual phages, and were able to examine the post-infection decision in real-time under the microscope, at the level of individual phages and cells 5 . (
  • This includes the creation of fluorescent phages, infection of the cells, imaging under the microscope and data analysis. (
  • The biology of phage infection has been extensively studied since the beginning of the 20th century. (
  • To investigate the biology of phage infection in complex bacterial communities, researchers followed phage dynamics in communities harboring phage-resistant (R) and phage-sensitive (S) bacteria, a common scenario in nature. (
  • Our work indicates that, similarly to the remarkable arsenal of entry and spreading strategies employed by viruses, phages utilize alternative, as yet unidentified spreading mechanisms, which could expedite the infection process and promote phage spread within cells of the same and different species," said PhD student Elhanan Tzipilevich, who carried out this research. (
  • When phage lambda infects a bacterial cell, which of the following are involved in its "decision" to undergo a lytic or a lysogenic infection? (
  • Cro binding first to all of the operator sites will cause the phage to undergo a lytic infection. (
  • It is well known that cells can be made susceptible to infection by providing DNA encoding the virus receptor. (
  • How resistant and sensitive bacteria in mixed communities respond to phage infection has not been well studied. (
  • While antibiotics have revolutionized medicine and are often very effective in stopping bacterial infection, well-developed phages could have several advantages over antibiotics. (
  • Because phage kills with a narrow scope, it could be used to cure an infection without disturbing the community of beneficial bacteria in our body. (
  • We present the genome sequences of Salmonella enterica tailed phages Sasha, Sergei, and Solent. (
  • The proteome of these phages was annotated by comparative analyses within the phage group itself and with the known sequences of three S. aureus lytic phages, 44AHJD, P68, and K ( 13 , 14 ). (
  • The trend for prophage genome inactivation was even more evident for the remaining five prophage sequences that showed massive losses of prophage DNA. (
  • They spontaneously generate miniphages of about 1 kb (2, 3), but they can also comprise artificial DNA sequences up to a length of 15 kb, if the phage packaging signal is provided (4). (
  • Complete Genome Sequences of 18 Paenibacillus larvae Phages from the Western United States. (
  • 30. ArrayOme- & tRNAcc-facilitated mobilome discovery: comparative genomics approaches for identifying rich veins of novel bacterial DNA sequences (Hong-Yu OU). (
  • These recombinant molecules are taken up by a host bacterium by transformation, creating a DNA library. (
  • During the lysogenic pathway, a lambda phage containing virus DNA attaches itself onto a host bacterium cell containing a plasmid. (
  • The system comprising bacteriophage (phage) lambda and the bacterium E. coli has long served as a paradigm for cell-fate determination 1,2 . (
  • Bacteriophage T4 is a virulent phage, which always lyses and kills its host bacterium. (
  • It lands on a bacterium, pierces the cell membrane and injects its DNA into the cell. (
  • Genome-length DNA molecules are then cut out of a larger, multigenome concatemer and packaged into capsids. (
  • DNA molecules adsorbed onto cationic fluid lipid membranes remain laterally diffusive. (
  • The periodically structured membranes revealed the ability to stretch long DNA molecules. (
  • The DNA stretching phenomenon can be elucidated in terms of a curvature dependent potential energy attained by the adsorbed DNA molecules. (
  • This process involves a molecular exchange driven by membrane vesicles (MVs), in which phage-resistant cells transiently gain phage attachment molecules released from neighboring phage-sensitive cells. (
  • Circular DNA molecules which contain a replicon that is based on the F factor. (
  • It is used for resolving DNA molecules of a range of sizes. (
  • A collection of cDNA molecules extracted from a particular organism, tissue or developmental stage and cloned into a DNA vector population. (
  • 1979). The genome of B. subtilis phage SSP1: the topology of DNA molecules. (
  • Pathogenic mitochondrial DNA (mtDNA) mutations often co‐exist with wild‐type molecules (mtDNA heteroplasmy). (
  • We obtained two crystal structures of a ternary complex BGT-UDP-DNA at 1.8A and 2.5A resolution, one with a Tris molecule and the other with a metal ion at the active site. (
  • We purify stable, mutant phage heads with a partially leaked mature DNA molecule. (
  • In any DNA molecule, the amounts of adenine and thymine are always the same while the amounts of guanine and cytosine are always the same. (
  • 17 , 18 ] The motor is geared by six copies of an RNA molecule called pRNA (packaging RNA)[ 19 ] and the ATPase gp16. (
  • 20 ] The high efficiency of in vitro DNA packaging up to 90%[ 17 , 18 , 21 , 22 ] and the feasibility to turn the motor on and turn off with γ -S-ATP[ 23 ] has enabled the single-molecule measurement of motor velocities and forces using an optical trap. (
  • If the cutting mechanism recognises slightly more than one genome length, each resultant DNA molecule has two letters (as schematised) repeated at the beginning and end of the molecule. (
  • DNA is a directional molecule. (
  • A circular DNA molecule that is replicated and segregated by the same mechanisms as the chromosome. (
  • The number of paired bases is a way of describing the length of a DNA molecule. (
  • Connected to, on the same DNA molecule. (
  • To purify a target DNA molecule from a reaction mixture (e.g. (
  • 4. The composition of claim 1 , wherein the target nucleic acid is a DNA molecule. (
  • 10. The kit of claim 9 , wherein the target nucleic acid is a DNA molecule. (
  • Ebola viruses don't use DNA as their information storage material , but the related molecule RNA. (
  • The lambda phage releases into the host cell where it is integrated into the host's genome. (
  • The lytic phages have been converted into phage spheroids by contact with water-chloroform interface. (
  • Once lytic phages are changed into spheroids, they retain their strong lytic activity and show high bacterial capture capability. (
  • The cos site of the bacteriophage λ chromosome contains the sites required for DNA processing and packaging during virion assembly. (
  • We show that it uses a pac site-directed headful packaging mechanism that results in virion chromosomes that are circularly permuted and about 13% terminally redundant. (
  • Once the DNA is packaged, the terminase detaches from the connector and the tail replaces it to finish maturation of the virion. (
  • The prohead structure may take a different shape from the head of a mature virion, as seen with the prohead of Bacillus subtilis phage φ29. (
  • The final phase-maturation, which overlaps with packaging-consists of programmed structural changes that convert the provirion into an infectious, virion. (
  • Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. (
  • Visualization of phage virions by transmission electron microscopy established that this phage belongs to the family Siphoviridae and possesses a long tail fiber, previously unseen in dairy lactococcal phages. (
  • Most published S. aureus phages belong to the Siphoviridae family of temperate, tailed bacterial viruses. (
  • Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. (
  • Morphological observation suggested that the phage belongs to the Siphoviridae family. (
  • In the new work reported this week, researchers have evaluated whether the energy thus stored is sufficient to permit phage DNA ejection, or only to initiate that process. (
  • The researchers used fluorescently labeled phage DNA to investigate in real time (and with a resolution time of 750 milliseconds) the dynamics of DNA ejection from single phages. (
  • The ejected DNA was measured at different stages of the ejection process after being stretched by applied hydrodynamic flow. (
  • Pausing times were observed during ejection, and ejection was transiently arrested at definite positions of the genome in close proximity to genetically defined physical interruptions in the DNA. (
  • The authors discuss the relevance of this stepwise ejection to the transfer of phage DNA in vivo. (
  • With this setup, we succeeded for the first time in visualizing the dynamics of the DNA ejection in real time. (
  • Temperature and ionic conditions control the mechanical properties of virally encapsidated DNA and act as a switch between synchronized and desynchronized genome ejection dynamics in a phage population. (
  • This portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection. (
  • A notable illustration of such prophage-plasmid coevolution is the similarity between the genome of a large phage 0305f8-36, isolated from B. thuringiensis and a contig of genome of the strain B. weihenstephanensis KBAB4 [ 13 , 14 ]. (
  • GTAs clearly have the potential to drive bacterial evolution and the spread of antibiotic resistance but discovery of novel GTAs is challenging because of their similarity to phages and lack of standardized detection methods. (
  • Participates also in T7 DNA packaging, host DNA degradation and phage genetic recombination. (
  • Phage transduction is used to move selectable genetic markers from one "donor" strain to another "recipient" strain. (
  • Nat Sternberg, among others, pioneered the use of phage P1 to move genetic elements in E. coli and the use of the Cre/Lox system from P1 for controlled recombination. (
  • We have found that a bacteriophage can transfer genetic elements, or DNA, between unrelated bacterial species in a way that was really not expected,' Novick says. (
  • It's the ideal specimen: It doesn't kill the host cell, scientists can vary the length of DNA that they're packaging (M13 packages genetic messages), and it has been engineered to get its DNA into mammalian cells. (
  • It has become clear, using rodent models as biological tools, that genetic instability in the form of gross DNA rearrangements or point mutations accumulate in the liver with age. (
  • One way to circumvent bacterial resistance is through the genetic modification of exterior phage components-an art in which Lu is a "master," says Marraffini. (
  • The present invention relates generally to polynucleotides and DNA and RNA probes, their preparation and their use in genetic characterization. (
  • Bill joined the Biology Department at BNL in December of 1964, where he has continued research on DNA physical chemistry and molecular genetics ever since. (
  • Understanding the mechanistic differences between phage and GTAs from a biochemical, structural and molecular point of view is key challenge we are looking to address with potential implications for bacterial evolution, antibiotic resistance and biotechnology. (
  • The researchers show how phage-sensitive bacteria harboring phage receptor can deliver the receptor to nearby phage-resistant cells that lack the phage receptor, via a molecular transfer they call "acquisition of sensitivity" (ASEN). (
  • This allows us to measure DNA translocation and the forces generated by the molecular motor in real time. (
  • This is the first report of a P. phenolica -infecting phage, and this phage genome study will provide useful information for further molecular research on P. phenolica and its phage, as well as their interactions. (
  • Phage λ chromosomes are 48.5-kb duplexes with 12-base-long, single-stranded extensions at the 5′ ends of the strands. (
  • Schaller, H., Beck, E. and Takanami, M. (1978) in: "The Single-Stranded DNA phages" Cold Spring Harbor Laboratory, Cold Spring Harobor pp. 139. (
  • The length distribution of the ejected DNA was analyzed and characteristic peaks were found at positions that coincided with the position of single-stranded interruptions (nicks) of the phage genome. (
  • our single stranded vector DNA. (
  • We then harvested the phage from the lysed culture of E. coli, and isolated our single stranded vector DNA. (
  • First, restricted and ligated DNA is encapsidated in vitro. (
  • For λ wild-type DNA the efficiency of in vitro packaging (10 6 to 10 7 plaques produced per μg of added DNA) is equal to, or better than, the standard CaCl 2 transfection method. (
  • Using this vector and in vitro packaging, several E. coli and phage P1 endo R.EcoRI fragments were cloned. (
  • this packaging activity can be replicated in vitro. (
  • We discover here a packaging ATPase-free, in vitro model for packaged DNA length quantization. (
  • 16 ] The DNA packaging motor of the bacterial virus phi29 is particularly attractive since it is relatively simple in structure and can be assembled in vitro using purified components. (
  • T7 RNA Polymerase is used for in vitro mRNA synthesis and is highly specific for the T7 phage promoter. (
  • The 99 KD enzyme catalyzes in vitro RNA synthesis from a cloned DNA sequence under the T7 promoters. (
  • Adriaenssens EM, Mattheus W, Cornelissen A, Shaburova O, Krylov VN et al (2012) Complete genome sequence of the giant Pseudomonas phage Lu11. (
  • RN [2] RT The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. (
  • This PhD thesis presents a fluorescence microscopy study about deoxyribose nucleic acid (DNA) in confined geometries. (
  • In that case, which sense (+/-) would have the phage nucleic acid when it has been integrated in the bacterial genome? (
  • After a concatemer's cosN is cut, terminase remains bound to the resulting cosB -containing DNA end, which is the left end of the chromosome to be packaged. (
  • The terminase-λDNA complex binds to the portal vertex of a prohead, and translocation of the DNA into the shell ensues. (
  • Translocation moves the DNA-packaging complex along the DNA until the next cos is encountered and the terminase docked at the portal vertex recognizes and cuts the downstream cos . (
  • Following cleavage, terminase undocks from the newly filled head and remains bound to the left end of the next chromosome along the concatemer, sponsoring its packaging. (
  • The terminase is composed of two subunits (a large and a small) and the small subunit recognizes the DNA to be encaspidated. (
  • Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA. (
  • and binds to the terminase subunits to form the packaging machine. (
  • Once a phage population has been generated from a donor host, the phage are used to infect a recipient host. (
  • Studies conducted to determine if the phage-encoded methylase confers host DNA methylation showed that the two S. flexneri strains analyzed encode their own Dam methylase. (
  • This injection notion arose naturally from the classic image of a T4 phage with its contractile tail, poised syringe-like on the surface of its soon-to-be host E. coli . (
  • After the phage tail attaches to the host receptors, the tail penetrates the cell membrane. (
  • A recent report relates the evolution of temperate phages and the regulatory elements involved in adaptation of B. anthracis to the animal host [ 7 ]. (
  • The phage DNA is then incorporated into the host chromosome and is replicated along with the rest of the host's DNA and remains inactive. (
  • The progeny DNA is then released from the host genome and is enclosed into virus packages. (
  • Once packaging is complete, DNA-containing capsids are enveloped and released from the host cell. (
  • The fibres attach to the host cell surface, and the phage DNA is injected into the cell through the sheath. (
  • It instructs the host to build copies of the phage (progeny, in cell). (
  • It is then packaged in the progeny, which are released when the host bursts. (
  • The Lysinibacillus is host for phage G ( Lysinibacillus PGH). (
  • A broad spectrum of different host ranges could be determined for several phages that lysed up to 24 different and in part highly antibiotic resistant strains. (
  • The three phages exhibit different patterns of domain duplication in the N-terminus of the tail fiber, which are involved in determination of the host range. (
  • Bystander Phage Therapy: Inducing Host-Associated Bacteria to Produce Antimicrobial Toxins against the Pathogen Using Phages. (
  • Using B. thetaiotaomicron strains that express defined subsets of CPSs, we show that CPSs dictate host tropism for these phages and that expression of non-permissive CPS variants is selected under phage predation, enabling survival. (
  • During the lysogenic response, the circular λ DNA is inserted into the host chromosome by a site-specific recombination event between the phage att site ( Fig. 2A ) and a cognate site on the host genome. (
  • Lipopolysaccharides on the external cell wall of the host cell provide recognition for the Phage which orients itself, perpendicular to the cell, using it's 6 tail fibers. (
  • If the host cell is a lysogen for the appropriate phage, prophage induction excises the SaPI, as well. (
  • The idea is to utilize phages that are host specific and can only destroy the disease-producing bacteria. (
  • Lastly, the phage produces toxic chemicals that rupture the bacterial host from inside out, releasing its newly made children to the outside to infect even more bacteria (Figure 1). (
  • When that bacteriophage infects another host, the bit of bacterial DNA gets incorporated into the new host's genome in a process called specialized transduction. (
  • Assembly of the T4 DNA polymerase holoenzyme. (
  • 7. The composition of claim 1 , further comprising a thermostable DNA polymerase. (
  • 13. The kit of claim 9 , further comprising a thermostable DNA polymerase. (
  • Bacteriophage T7 RNA Polymerase is a DNA-dependent RNA polymerase that is highly specific for the T7 phage promoters. (
  • 1X RNAPol Reaction Buffer, supplemented with 0.5 mM each ATP, UTP, GTP, CTP, and DNA template containing the T7 RNA Polymerase promoter. (
  • The cytosol may also contain various episomes (small circular chromosomes), some called plasmids, and others called (bacterio)phages, which are bacterial viruses. (
  • Destroying the host's DNA releases nucleotide building blocks, from which phage DNA is synthesised. (
  • Digest the DNA with a restriction enzyme. (
  • Insert the fragments of DNA into vectors that were cut with the same restriction enzyme. (
  • The protected DNA segment has quantized lengths, based on restriction endonuclease analysis: six sharp bands of DNA missing 3.7-12.3% of the last end packaged. (
  • If you need to transduce a strain with an active restriction system, I recommend including a control using the same phage to transduce the marker into a strain that does not have that restriction. (
  • Restriction mapping and sequence analysis revealed that the phage genome has cos sites at the termini. (
  • Physical maps of the recombinant plasmids were prepared showing restriction endonuclease sites within the inserted DNA fragments. (
  • There are also intracellular barriers such as phage restriction mechanisms and, as noted earlier, the bacterial immune system called CRISPR (clustered regularly interspaced short palindromic repeats). (
  • The depolarization model proposes that cosQ acts in presenting a gpA subunit to the bottom strand of cosN by forming a bend in the region of DNA between cosQ and cosN , forming a loop for cosQ and cosN to be aligned in the same orientation. (
  • Hydrogen bond formation allow double strand DNA to form two complementary single strands. (
  • DNAP will use the negative strand as a template to make positive sense DNA. (
  • RecA plays a central role in homologous recombination and DNA repair, catalyzing a complex set of DNA strand transfer reactions. (
  • 3' refers to the end of a single-strand of DNA that has a hydroxyl group on the 3' carbon of the sugar. (
  • DNA polymerases extend a DNA strand by adding nucleotides to the 3' end (in the 5' to 3' direction). (
  • 5' refers to the end of a single-strand of DNA to which the phosphate group is attached. (
  • Calf Intestinal alkaline Phosphatase, an enzyme for removing the phosphate group from the 5' end of a strand of DNA. (
  • DNA enters bacterial cytosol as double strand. (
  • The replicase enzyme makes copies of both plus and minus strands, though the latter are only used as a template to make more (+) strand for both translation and packaging into phage. (
  • E. coli with active UNG and DUT has the ability to degrade sections of DNA that contain uracil, and replace them with sections complementary to the opposite strand that contain thymine. (
  • Thus, the native Kumamolisin strand that still contained the U's from the UNG-/DUT- strain was degraded, and the new cells incorporated our desired mutation when synthesizing new DNA from the variant strand. (
  • Postdoctoral research in Dale Kaiser's group in the Department of Biochemistry, Stanford University School of Medicine, introduced him to bacteriophage biochemistry and genetics, and continuing work on DNA physical chemistry, helped by stimulating interactions with Buzz Baldwin, Bob Lehman and David Hogness, led to his first important paper "Sedimentation Studies of the Size and Shape of DNA" in 1965. (
  • To understand the interactions between these organisms and the phages that infect them, a number of phages were isolated against lactococcal strains of non-dairy origin. (
  • The created biosensors have been examined by a quartz crystal microbalance with dissipation tracking (QCM-D) to evaluate bacteria-phage interactions. (
  • Studying phage a primitive class of virus that infects bacteria by in. (
  • Despite the obvious importance of phages for the biology of S. aureus , epidemiological data on the prevalence of phages in this species are limited ( 28 , 33 ). (
  • This is the first time that phages have been observed to serve as shuttle vehicles for bacterial toxins between different species. (
  • Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. (
  • First, phages are specific to one species of bacteria and are therefore unlikely to disturb beneficial microbe living in our guts. (
  • Comparative genome analysis supports the conclusion that ΦL47 is a new member of the 949 lactococcal phage group which currently includes the dairy Φ949. (
  • In addition to the importance of plasmids, carrying the toxins, it was also suggested that the temperate phages can be involved in the adaptation of these bacteria to animal hosts [ 1 , 7 ]. (
  • Microbes have been known to gain antibiotic resistance through the transfer of plasmids, extra-chromosomal pieces of DNA that can be shuttled between unrelated bacteria. (
  • Because cosQ mutants fail to cut the downstream cos and fail to stop translocation at cos , the shell is filled to capacity, and because the protruding DNA prevents tail attachment, the cosQ defect is lethal. (
  • We use directed evolution to isolate a five-site T3 point mutant that hyper-produces tail-free capsids with mature DNA (heads). (
  • The tail contracts, the DNA squirts into the cell. (
  • Now the DNA-one end already within the tail tube-is pushed by the internal pressure into the cell where it sets to work. (
  • To take a visual trip through the phage T4 tail tube, click here , and then double-click the image dis- played. (
  • Analysis of three marker modules (lysogeny, tail, and lysis) for phage functional units revealed that these phages exhibit different degrees of genome mosaicism. (
  • Each phage consists of a large DNA- containing head and a tail composed of a central sheath with several fibres. (
  • 2008) Evidence for bacteriophage T7 tail extension during DNA injection. (
  • The phage sequence information reported herein constitutes a valuable resource to better study the mechanism of genome and proteome diversity in phages. (
  • Sequence analysis also suggests that SfV encodes multiple DNA methylases, and experiments confirmed that orf-41 encodes a Dam methylase. (
  • A DNA sequence which, when transcribed into mRNA, is recognized by the ribosome as a signal to initiate translation from the subsequent start codon 8 bases downstream. (
  • A method of determining the DNA sequence of a chromosome by extending out from a known region, designing a new sequencing primer to read out from the newly sequenced region and continuing until the desired section of DNA has been sequenced. (
  • DNA imported is not based upon sequence specificity. (
  • DNA is cut on opposite strands at the two ends of the target sequence. (
  • Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut. (
  • This rDNA can be transferred into bacteria like E. coli or into yeast through a process called transformation, so that many copies or clones of the DNA sequence of interest are made. (
  • Empty phage capsids form at the bacterial cytoplasmic membrane, then migrate to the compartment where they attach firmly to the surface. (
  • Furthermore, phage SPP1 can infect resistant cells that have been incubated with membrane vesicles from a susceptible strain - in the absence of intact susceptible cells. (
  • Rather than stopping bacteria from doing one specific process like in the case of antibiotics, phages actively destroy the bacteria's cell wall and cell membrane and kill bacteria by making many holes from the inside out. (
  • For the selection of carcinoma-specific peptides membrane proteome of HNO97 tumor cells fractionated by the ProteomeLab PF2D system and corresponding HNO97 cells were deployed for an alternating biopanning using a sunflower trypsin inhibitor1-based phage display (SFTI8Ph) library. (
  • Phages P1 and T4 and the newly isolated E. coli phage EC10 were used as vectors. (
  • He received a B.S. in Biophysics from Yale University and a Ph.D. in Biophysics from the California Institute of Technology, where he worked in the group of James Bonner on "Studies on the DNA of Bacteriophage T7" with guidance from Paul Ts'o, Jerry Vinograd and Bob Sinsheimer, the person who introduced him to bacteriophage T7. (
  • Newly replicated DNA is then packaged into preformed capsids. (
  • In this report we describe a coliphage λ vector system for cloning endo R. EcoRI DNA fragments. (
  • The fragments are then inserted into the vector using DNA ligase. (
  • Use the enzyme DNA ligase to seal the DNA fragments into the vector. (
  • VSH-1 is a mitomycin C-inducible, nonlytic, phage-like agent that packages random 7.5 kb fragments of the Brachyspira hyodysenteriae genome. (
  • The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. (
  • A variable-length DNA segment leaks from some mutant heads, based on DNase I-protection assay and electron microscopy. (
  • In 2008, Sidhu left sunny California for the Donnelly Centre in Toronto to be at the forefront of genomics research and use its insights to find medically useful antibodies from the deluge produced by phage display. (
  • DNA translocation across the barriers of recipient cells is not well understood. (
  • and (iv) DNA translocation. (
  • Ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine and other oxidized methylcytosines, intermediates in DNA demethylation. (
  • It is a satellite virus, requiring P2-related helper phage to grow lytically. (
  • It is a satellite virus which cannot engage in lytic growth without the presence of a P2-related helper phage. (
  • Remarkably, different SaPIs use different combinations of these three mechanisms, depending on which particular helper phage they are exploiting," said Christie. (
  • Traditionally, S. aureus phages were characterized according to their lytic activity, morphology, and serological properties ( 1 , 28 ). (
  • Due to the different properties and advantages, Creative Biolabs is pleased to tailor the most appropriate phage display system (M13, T4 or T7) to meet our customers' demands. (
  • The superantigens are encoded between the phage lysin and the right attachment site of the prophage genome. (
  • In these prophage remnants only 13-0.3 kb of putative prophage DNA was detected. (
  • Researchers created lysogens that carried a SaPI and a prophage with a mutation that prevented its DNA from packaging. (
  • Known as a prophage, this stretch of foreign DNA can persist for generations before activating. (
  • Once activated, the prophage cuts itself out of the bacterial genome, replicates and then packages its DNA into phages. (
  • Occasionally, there's an error in the cutting, and a small portion of the bacterial genome gets copied and packaged alongside the prophage. (
  • is required for the termination of chromosome packaging. (
  • The DNA is carried on the genophore, a circular chromosome, in an ill defined area of the cytosol called the nucleoid. (
  • When a mixed culture of resistant and susceptible B. subtilis cells were infected with phage SPP1, both types of cells became infected and killed. (
  • For the mechanics model, this requires invoking some other mechanism to get the DNA to the finish line. (
  • 2008. The Structure of the Phage T4 DNA Packaging Motor Suggests a Mechanism Dependent on Electrostatic Forces. (
  • Now, in new research in the Jan. 12 edition of Cell, researchers at the Hebrew University of Jerusalem's Faculty of Medicine provide the first demonstration of a mechanism by which bacteria entirely resistant to a given phage become susceptible to it upon co-incubation with sensitive bacteria. (
  • However, many SaPIs don't encode a mechanism for their own excision (e.g., they have no ORF resembling xis of phage lambda ) and thus they cannot excise spontaneously. (