Bacteriophage T4
Bacteriophage T7
T-Phages
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.
Bacteriophage T3
Escherichia coli
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.
Bacteriophage lambda
Lysogeny
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.
Bacteriophage mu
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.
Mutation
Base Sequence
Bacteriophage phi X 174
Bacteriophage phi 6
DNA-Directed RNA Polymerases
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
Molecular Sequence Data
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.
DNA Primase
Viral Tail Proteins
Bacteriophage M13
DNA-Directed DNA Polymerase
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
Bacteriophage P2
Genes
DNA, Single-Stranded
Genetics, Microbial
Siphoviridae
Bacteriolysis
Bacteriophage Typing
Plasmids
Bacteriophage P1
Recombination, Genetic
Polynucleotide Ligases
DNA Helicases
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
DNA Packaging
Salmonella Phages
Virus Replication
Amino Acid Sequence
Centrifugation, Density Gradient
RNA Phages
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.
Adsorption
Nucleic Acid Conformation
Chloramphenicol
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)
Bacteriophage PRD1
Pseudomonas Phages
DNA Restriction Enzymes
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.
Templates, Genetic
RNA Nucleotidyltransferases
Cloning, Molecular
Transcription, Genetic
Bacillus Phages
Thymine Nucleotides
Genetic Complementation Test
Exonucleases
Phosphorus Isotopes
Temperature
Microscopy, Electron
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.
Nucleic Acid Denaturation
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.
Muramidase
A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17.
RNA Ligase (ATP)
Endodeoxyribonucleases
Radiation Effects
Levivirus
Chromosome Mapping
Ultraviolet Rays
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.
Oligoribonucleotides
DNA Nucleotidyltransferases
DNA
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).
Viral Plaque Assay
Method for measuring viral infectivity and multiplication in CULTURED CELLS. Clear lysed areas or plaques develop as the VIRAL PARTICLES are released from the infected cells during incubation. With some VIRUSES, the cells are killed by a cytopathic effect; with others, the infected cells are not killed but can be detected by their hemadsorptive ability. Sometimes the plaque cells contain VIRAL ANTIGENS which can be measured by IMMUNOFLUORESCENCE.
Site-Specific DNA-Methyltransferase (Adenine-Specific)
An enzyme responsible for producing a species-characteristic methylation pattern on adenine residues in a specific short base sequence in the host cell DNA. The enzyme catalyzes the methylation of DNA adenine in the presence of S-adenosyl-L-methionine to form DNA containing 6-methylaminopurine and S-adenosyl-L-homocysteine. EC 2.1.1.72.
Binding Sites
Electrophoresis, Polyacrylamide Gel
Viral Structural Proteins
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).
Models, Molecular
Prophages
Electrophoresis, Agar Gel
Transduction, Genetic
Inovirus
Endonucleases
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Deoxyribonucleotides
Suppression, Genetic
Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).
Genetic Code
DNA-Binding Proteins
Attachment Sites, Microbiological
Cell-Free System
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
Protein Binding
DNA, Recombinant
Cryoelectron Microscopy
Substrate Specificity
Operon
Promoter Regions, Genetic
Restriction Mapping
F Factor
Protein Biosynthesis
Nucleotides
Polynucleotide 5'-Hydroxyl-Kinase
Viral Interference
DNA, Circular
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)
Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Transferases
Transferases are enzymes transferring a group, for example, the methyl group or a glycosyl group, from one compound (generally regarded as donor) to another compound (generally regarded as acceptor). The classification is based on the scheme "donor:acceptor group transferase". (Enzyme Nomenclature, 1992) EC 2.
Gene Expression Regulation, Viral
Phosphorus Radioisotopes
Rifampin
A semisynthetic antibiotic produced from Streptomyces mediterranei. It has a broad antibacterial spectrum, including activity against several forms of Mycobacterium. In susceptible organisms it inhibits DNA-dependent RNA polymerase activity by forming a stable complex with the enzyme. It thus suppresses the initiation of RNA synthesis. Rifampin is bactericidal, and acts on both intracellular and extracellular organisms. (From Gilman et al., Goodman and Gilman's The Pharmacological Basis of Therapeutics, 9th ed, p1160)
Receptors, Virus
Centrifugation, Zonal
DNA Repair
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
Exodeoxyribonucleases
Cystoviridae
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
DNA Ligases
Virus Assembly
Bacteriophage Pf1
Sucrose
DCMP Deaminase
Oligodeoxyribonucleotides
Open Reading Frames
Oligonucleotides
Ribonucleoside Diphosphate Reductase
RNA, Bacterial
Caudovirales
Chromosomes, Bacterial
Colicins
Crosses, Genetic
Thioredoxins
Hydrogen-donating proteins that participates in a variety of biochemical reactions including ribonucleotide reduction and reduction of PEROXIREDOXINS. Thioredoxin is oxidized from a dithiol to a disulfide when acting as a reducing cofactor. The disulfide form is then reduced by NADPH in a reaction catalyzed by THIOREDOXIN REDUCTASE.
Exodeoxyribonuclease V
DNA Primers
Adenosine Triphosphatases
Aminacrine
Sequence Analysis, DNA
Adenosine Triphosphate
RNA, Messenger
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Species Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Magnesium
Macromolecular Substances
Genes, Regulator
Rho Factor
Crystallography, X-Ray
Sequence Homology, Amino Acid
Deoxyribonuclease (Pyrimidine Dimer)
Sequence Homology, Nucleic Acid
Morphogenesis
Ribonucleotides
Chromatography, DEAE-Cellulose
Virion
Cesium
Mutagenesis
RNA, Transfer
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Biological Therapy
Drug Resistance, Microbial
Host Specificity
Deoxycytidine Monophosphate
Enzyme Induction
Structure-Activity Relationship
Myoviridae
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Viral Regulatory and Accessory Proteins
A broad category of viral proteins that play indirect roles in the biological processes and activities of viruses. Included here are proteins that either regulate the expression of viral genes or are involved in modifying host cell functions. Many of the proteins in this category serve multiple functions.
Sodium Dodecyl Sulfate
Phosphotungstic Acid
Tungsten hydroxide oxide phosphate. A white or slightly yellowish-green, slightly efflorescent crystal or crystalline powder. It is used as a reagent for alkaloids and many other nitrogen bases, for phenols, albumin, peptone, amino acids, uric acid, urea, blood, and carbohydrates. (From Merck Index, 11th ed)
Rec A Recombinases
A family of recombinases initially identified in BACTERIA. They catalyze the ATP-driven exchange of DNA strands in GENETIC RECOMBINATION. The product of the reaction consists of a duplex and a displaced single-stranded loop, which has the shape of the letter D and is therefore called a D-loop structure.
Micrococcus
Mutagenesis, Site-Directed
RNA
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Bacteriophage phiYeO3-12, specific for Yersinia enterocolitica serotype O:3, is related to coliphages T3 and T7. (1/25)
Bacteriophage phiYeO3-12 is a lytic phage of Yersinia enterocolitica serotype O:3. The phage receptor is the lipopolysaccharide O chain of this serotype that consists of the rare sugar 6-deoxy-L-altropyranose. A one-step growth curve of phiYeO3-12 revealed eclipse and latent periods of 15 and 25 min, respectively, with a burst size of about 120 PFU per infected cell. In electron microscopy phiYeO3-12 virions showed pentagonal outlines, indicating their icosahedral nature. The phage capsid was shown to be composed of at least 10 structural proteins, of which a protein of 43 kDa was predominant. N-terminal sequences of three structural proteins were determined, two of them showing strong homology to structural proteins of coliphages T3 and T7. The phage genome was found to consist of a double-stranded DNA molecule of 40 kb without cohesive ends. A physical map of the phage DNA was constructed using five restriction enzymes. The phage infection could be effectively neutralized using serum from a rabbit immunized with whole phiYeO3-12 particles. The antiserum also neutralized T3 infection, although not as efficiently as that of phiYeO3-12. phiYeO3-12 was found to share, in addition to the N-terminal sequence homology, several common features with T3, including morphology and nonsubjectibility to F exclusion. The evidence conclusively indicated that phiYeO3-12 is the first close relative of phage T3 to be described. (+info)Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase. (2/25)
Insertion of the T3 DNA polymerase thioredoxin binding domain (TBD) into the distantly related thermostable Taq DNA polymerase at an analogous position in the thumb domain, converts the Taq DNA polymerase from a low processive to a highly processive enzyme. Processivity is dependent on the presence of thioredoxin. The enhancement in processivity is 20-50-fold when compared with the wild-type Taq DNA polymerase or to the recombinant polymerase in the absence of thioredoxin. The recombinant Taq DNA pol/TBD is thermostable, PCR competent and able to copy repetitive deoxynucleotide sequences six to seven times more faithfully than Taq DNA polymerase and makes 2-3-fold fewer AT-->GC transition mutations. (+info)The genome sequence of Yersinia pestis bacteriophage phiA1122 reveals an intimate history with the coliphage T3 and T7 genomes. (3/25)
The genome sequence of bacteriophage phiA1122 has been determined. phiA1122 grows on almost all isolates of Yersinia pestis and is used by the Centers for Disease Control and Prevention as a diagnostic agent for the causative agent of plague. phiA1122 is very closely related to coliphage T7; the two genomes are colinear, and the genome-wide level of nucleotide identity is about 89%. However, a quarter of the phiA1122 genome, one that includes about half of the morphogenetic and maturation functions, is significantly more closely related to coliphage T3 than to T7. It is proposed that the yersiniophage phiA1122 recombined with a close relative of the Y. enterocolitica phage phiYeO3-12 to yield progeny phages, one of which became the classic T3 coliphage of Demerec and Fano (M. Demerec and U. Fano, Genetics 30:119-136, 1945). (+info)Characterization of bacteriophage T3 DNA ligase. (4/25)
DNA ligases of bacteriophage T4 and T7 have been widely used in molecular biology for decades, but little is known about bacteriophage T3 DNA ligase. Here is the first report on the cloning, expression and biochemical characterization of bacteriophage T3 DNA ligase. The polyhistidine-tagged recombinant T3 DNA ligase was shown to be an ATP-dependent enzyme. The enzymatic activity was not affected by high concentration of monovalent cations up to 1 M, whereas 2 mM ATP could inhibit its activity by 50%. Under optimal conditions (pH 8.0, 0.5 mM ATP, 5 mM DTT, 1 mM Mg(2+) and 300 mM Na(+)), 1 fmol of T3 DNA ligase could achieve 90% ligation of 450 fmol of cohesive dsDNA fragments in 30 min. T3 DNA ligase was shown to be over 5-fold more efficient than T4 DNA ligase for ligation of cohesive DNA fragments, but less active for blunt-ended DNA fragments. Phylogenetic analysis showed that T3 DNA ligase is more closely related to T7 DNA ligase than to T4 DNA ligase. (+info)In vivo hydrolysis of S-adenosylmethionine induces the met regulon of Escherichia coli. (5/25)
Regulation of methionine biosynthesis in Escherichia coli involves a complex of the MetJ aporepressor protein and S-adenosylmethionine (SAM) repressing expression of most genes in the met regulon. To test the role of SAM in the regulation of met genes directly, SAM pools were depleted by the in vivo expression of the cloned plasmid vector-based coliphage T3 SAM hydrolase (SAMase) gene. Cultures with in vivo SAMase activity were assayed for expression of the metA, B, C, E, F, H, J, K and R genes in cells grown in methionine-rich complete media as well as in defined media with and without l-methionine. In vivo SAMase activity dramatically induced expression between 11- and nearly 1000-fold depending on the gene assayed for all but metJ and metH, and these genes were induced over twofold. metJ : : Tn5 (aporepressor defective) and metK : : Tn5 (SAM synthetase impaired; produces <5 % of wild-type SAM) strains containing in vivo SAMase activity produced even higher met gene activity than that seen in comparably prepared cells with wild-type genes for all but metJ in a MetJ-deficient background. The SAMase-mediated hyperinduction of metH in wild-type cells and of the met genes assayed in metJ : : Tn5 and metK : : Tn5 cells provokes questions about how other elements such as the MetR activator protein or factors beyond the met regulon itself might be involved in the regulation of genes responsible for methionine biosynthesis. (+info)Compensatory evolution in response to a novel RNA polymerase: orthologous replacement of a central network gene. (6/25)
A bacteriophage genome was forced to evolve a new system of regulation by replacing its RNA polymerase (RNAP) gene, a central component of the phage developmental pathway, with that of a relative. The experiment used the obligate lytic phage T7 and the RNAP gene of phage T3. T7 RNAP uses 17 phage promoters, which are responsible for all middle and late gene expression, DNA replication, and progeny maturation, but the enzyme has known physical contacts with only 2 other phage proteins. T3 RNAP was supplied in trans by the bacterial host to a T7 genome lacking its own RNAP gene and the phage population was continually propagated on naive bacteria throughout the adaptation. Evolution of the T3 RNAP gene was thereby prevented, and selection was for the evolution of regulatory signals throughout the phage genome. T3 RNAP transcribes from T7 promoters only at low levels, but a single mutation in the promoter confers high expression, providing a ready mechanism for reevolution of gene expression in this system. When selected for rapid growth, fitness of the engineered phage evolved from a low of 5 doublings/h to 33 doublings/h, close to the expected maximum of 37 doublings/h. However, the experiment was terminated before it could be determined accurately that fitness had reached an obvious plateau, and it is not known whether further adaptation could have resulted in complete recovery of fitness. More than 30 mutations were observed in the evolved genome, but changes were found in only 9 of the 16 promoters, and several coding changes occurred in genes with no known contacts with the RNAP. Surprisingly, the T7 genome adapted to T3 RNAP also maintained high fitness when using T7 RNAP, suggesting that the extreme incompatibility of T7 elements with T3 RNAP is not an invariant property of divergence in these expression systems. (+info)Evolution and the complexity of bacteriophages. (7/25)
BACKGROUND: The genomes of both long-genome (> 200 Kb) bacteriophages and long-genome eukaryotic viruses have cellular gene homologs whose selective advantage is not explained. These homologs add genomic and possibly biochemical complexity. Understanding their significance requires a definition of complexity that is more biochemically oriented than past empirically based definitions. HYPOTHESIS: Initially, I propose two biochemistry-oriented definitions of complexity: either decreased randomness or increased encoded information that does not serve immediate needs. Then, I make the assumption that these two definitions are equivalent. This assumption and recent data lead to the following four-part hypothesis that explains the presence of cellular gene homologs in long bacteriophage genomes and also provides a pathway for complexity increases in prokaryotic cells: (1) Prokaryotes underwent evolutionary increases in biochemical complexity after the eukaryote/prokaryote splits. (2) Some of the complexity increases occurred via multi-step, weak selection that was both protected from strong selection and accelerated by embedding evolving cellular genes in the genomes of bacteriophages and, presumably, also archaeal viruses (first tier selection). (3) The mechanisms for retaining cellular genes in viral genomes evolved under additional, longer-term selection that was stronger (second tier selection). (4) The second tier selection was based on increased access by prokaryotic cells to improved biochemical systems. This access was achieved when DNA transfer moved to prokaryotic cells both the more evolved genes and their more competitive and complex biochemical systems. TESTING THE HYPOTHESIS: I propose testing this hypothesis by controlled evolution in microbial communities to (1) determine the effects of deleting individual cellular gene homologs on the growth and evolution of long genome bacteriophages and hosts, (2) find the environmental conditions that select for the presence of cellular gene homologs, (3) determine which, if any, bacteriophage genes were selected for maintaining the homologs and (4) determine the dynamics of homolog evolution. IMPLICATIONS OF THE HYPOTHESIS: This hypothesis is an explanation of evolutionary leaps in general. If accurate, it will assist both understanding and influencing the evolution of microbes and their communities. Analysis of evolutionary complexity increase for at least prokaryotes should include analysis of genomes of long-genome bacteriophages. (+info)Dispersing biofilms with engineered enzymatic bacteriophage. (8/25)
Synthetic biology involves the engineering of biological organisms by using modular and generalizable designs with the ultimate goal of developing useful solutions to real-world problems. One such problem involves bacterial biofilms, which are crucial in the pathogenesis of many clinically important infections and are difficult to eradicate because they exhibit resistance to antimicrobial treatments and removal by host immune systems. To address this issue, we engineered bacteriophage to express a biofilm-degrading enzyme during infection to simultaneously attack the bacterial cells in the biofilm and the biofilm matrix, which is composed of extracellular polymeric substances. We show that the efficacy of biofilm removal by this two-pronged enzymatic bacteriophage strategy is significantly greater than that of nonenzymatic bacteriophage treatment. Our engineered enzymatic phage substantially reduced bacterial biofilm cell counts by approximately 4.5 orders of magnitude ( approximately 99.997% removal), which was about two orders of magnitude better than that of nonenzymatic phage. This work demonstrates the feasibility and benefits of using engineered enzymatic bacteriophage to reduce bacterial biofilms and the applicability of synthetic biology to an important medical and industrial problem. (+info)
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Escherichia virus T3
... , also called bacteriophage T3 and T3 phage, is a bacteriophage capable of infecting susceptible bacterial ... FRASER, D; WILLIAMS, RC (Feb 1953). "Details of frozen-dried T3 and T7 bacteriophages as shown by electron microscopy". Journal ... "DNA packaging-associated hyper-capsid expansion of bacteriophage t3". Journal of Molecular Biology. 397 (2): 361-74. doi: ... T3+Phage at the US National Library of Medicine Medical Subject Headings (MeSH) v t e (Articles with short description, Short ...
Abortive initiation
... is typically studied in the T3 and T7 RNA polymerases in bacteriophages and in E. coli. Abortive initiation ...
Restriction modification system
Other viruses, such as bacteriophages T3 and T7, encode proteins that inhibit the restriction enzymes.[citation needed] To ... They found that bacteriophage growing within an infected bacterium could be modified, so that upon their release and re- ... This prevents infection by effectively destroying the foreign DNA introduced by an infectious agent (such as a bacteriophage). ... infection of a related bacterium the bacteriophage's growth is restricted (inhibited) (also described by Luria in his ...
Escherichia virus T4
His part was naming the bacteriophages into Type 1(T1), Type 2 (T2), Type 3 (T3), etc.[citation needed] The specific time and ... T4-like viruses Animation of T4 Bacteriophage Infecting E.coli Animation of T4 Bacteriophage DNA packaging (Articles with short ... "Genetic Recombinations Leading to Production of Active Bacteriophage from Ultraviolet Inactivated Bacteriophage Particles". ... Molecular Biology of Bacteriophage T4. ASM Press, Washington, DC. (The second T4 bible, go here, as well as Mosig and Eiserling ...
Genetically modified tomato
Agritope introduced an S-adenosylmethionine hydrolase (SAMase) encoding gene derived from the E. coli bacteriophage T3, which ...
Nuclease protection assay
T7 or T3. These promoters are recognized by DNA dependent RNA polymerases originally characterized from bacteriophages. The ...
Ellen Jorgensen
"Discrimination between bacteriophage T3 and T7 promoters by the T3 and T7 RNA polymerases depends primarily upon a three base- ...
List of MeSH codes (B04)
... bacteriophage n4 MeSH B04.123.150.700.070 - bacteriophage p22 MeSH B04.123.150.700.100 - bacteriophage t3 MeSH B04.123.150.700. ... bacteriophage n4 MeSH B04.280.090.700.070 - bacteriophage p22 MeSH B04.280.090.700.100 - bacteriophage t3 MeSH B04.280.090.700. ... bacteriophage t3 MeSH B04.123.205.891.200 - bacteriophage t4 MeSH B04.123.205.891.230 - bacteriophage t7 MeSH B04.123.230.070 ... bacteriophage p1 MeSH B04.123.205.305 - bacteriophage p2 MeSH B04.123.205.320 - bacteriophage phi x 174 MeSH B04.123.205.350 - ...
HindIII
The cleavage of this sequence between the AA's results in 5' overhangs on the DNA called sticky ends: 5'-A ,A G C T T-3' 3'-T T ... Their primary function is to protect the host genome against invasion by foreign DNA, primarily bacteriophage DNA. There is ...
T7 RNA polymerase
... swapping it out for one found in T3 RNAP makes the polymerase recognize T3 promoters instead. Similar to other viral nucleic ... T7 RNA Polymerase is an RNA polymerase from the T7 bacteriophage that catalyzes the formation of RNA from DNA in the 5'→ 3' ... Other members include phage T3 and SP6 RNA polymerases, the mitochondrial RNA polymerase (POLRMT), and the chloroplastic ssRNAP ... McAllister WT (1993). "Structure and function of the bacteriophage T7 RNA polymerase (or, the virtues of simplicity)". Cellular ...
Lung microbiota
The DNA-binding protein complex recognizes a discrete nucleotide sequence (5'-GGG ACT TTC T-3') in the upstream region of a ... These microorganisms include bacteria, fungi, viruses and bacteriophages. The bacterial part of the microbiota has been more ...
Phage-assisted continuous evolution
It relies on relating the desired activity of a target protein with the fitness of an infectious bacteriophage which carries ... This resulted in polymerases with ~3-4 orders of magnitude greater activity for the target promoter than the original T3 ... The central component of PACE is a fixed-volume vessel known as the "lagoon". The lagoon contains M13 bacteriophage vectors ... Brödel, A.K.; Isalan, M.; Jaramillo, A. (2018). "Engineering of biomolecules by bacteriophage directed evolution". Curr. Opin. ...
Yersinia infection - References | BMJ Best Practice US
The microbiome beyond the horizon of ecological and evolutionary theory | Nature Ecology & Evolution
Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc. Natl Acad. Sci. USA 110,10771-10776 (2013). ... A T3 and T7 recombinant phage acquires efficient adsorption and a broader host range. PLoS ONE 7, e30954 (2012). ... Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 6, 915- ...
DeCS
Bacteriophage T3 - Preferred Concept UI. M0027047. Scope note. Bacteriophage in the genus T7-like phages, of the family ... Coliphage T3 Enterobacteria phage T3 Phage T3 Phage, T3 Phages, T3 T3 Phage T3 Phages ... Coliphage T3. Enterobacteria phage T3. Phage T3. Phage, T3. Phages, T3. T3 Phage. T3 Phages. ... colifago T3 fago T3 fago T3 de enterobacterias Scope note:. Bacteriófago del género de fagos similares a T7, de la familia ...
Table 3 - Pathogenic Potential to Humans of Bovine Escherichia coli O26, Scotland - Volume 18, Number 3-March 2012 - Emerging...
pIRES...
Publication : USDA ARS
Results suggest that bacteriophage can be used as a dietary strategy to reduce the presence of SE in internal organs and also ... In spleen, T4 significantly reduced (P < 0.05) the bacteria from 0.94 in both T2 and T3 to 0.56 log cfu/gm. There was no ... Effect of dietary bacteriophage supplementation in internal organs, fecal excretion and ileal immune response in laying hens ... There was no significant effect of T3 on reduction of numbers of cecal SENAR. A significant reduction of SENAR (P < 0.05) was ...
Ceco/microbiologia
Dietary bacteriophages potentially can serve as a step to reduce Salmonella contamination of feed through direct lysis of the ... No significant differences in bird weight were observed between treatments d 0 to 42 (P > 0.05). However, T2 and T3 had lower ... Therefore, the dietary bacteriophage did not interfere with colonization or protection afforded by the live Salmonella vaccine. ... The objective of this study was to evaluate if dietary bacteriophages impacted the colonization of a live Salmonella vaccine. A ...
PRJNA631837 - - OmicsDI
Directed evolution of T3 and T7 bacteriophages for improved thermostability. ... Here the major capsid gene of the bacteriophage T7 (40-kb dsDNA) was replaced with the homologous gene of either T3 or K11, ... T3/7 is essentially T3 based, but a DNA fragment containing part of the tail fiber gene 17 is replaced by the T7 sequence. T3 ... The T3 and T7 recombinant phage carries altered tail fibers and acquires better adsorption efficiency than T3. How phages T3 ...
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Publications<...
Table 3 - Lineage-specific Virulence Determinants of Haemophilus influenzae Biogroup aegyptius - Volume 18, Number 3-March 2012...
Science Clips - Monday, June 28, 2010
Survival of bacteriophage MS2 on filtering facepiece respirator coupons. Fisher E, Shaffer R.. Appl Biosafety. 2010 Apr-Jun;15( ... Sappenfield WM, Peck MG, Gilbert CS, Haynatzka VR, Bryant T3.. Matern Child Health J. 2010 Jun 20.. ... Sappenfield WM, Peck MG, Gilbert CS, Haynatzka VR, Bryant T3.. Matern Child Health J. 2010 Jun 18.. ...
Effects on mRNA degradation by Escherichia coli transcription termination factor Rho and pBR322 copy number control protein Rop
Tau factor from Escherichia coli mediates accurate and efficient termination of transcription at the bacteriophage T3 early ... The Effects of Ionic Strength on Termination of Transcription of Dnas from Bacteriophages T4, T5 and T7 by Dna-Dependent Rna ... The effects of ionic strength on termination of transcription of DNAs from bacteriophages T4, T5 and T7 by DNA-dependent RNA ... were previously isolated based on their ability to block the growth of bacteriophage T4. Here we show that rho(nusD) strains ...
Suppression of growth of Fusarium verticillioides Niren. using strains of Trichoderma harzianum from maize (Zea mays) plant...
November | 2019 | Thrombin Inhibitor
Ackermann HW: Bacteriophage observations and evolution. Res Microbiol 2003,154(4):245-251.PubMedCrossRef 39. DeShazer D, Waag ... of the phage-associated novel superantigen gene speL in recent invasive and noninvasive Streptococcus pyogenes M3/T3 isolates ... Juhala RJ, Ford ME, Duda RL, Youlton A, Hatfull GF, Hendrix RW: Genomic sequences of bacteriophages HK97 and HK022: pervasive ... Hendrix RW, Hatfull GF, Smith MC: Bacteriophages with tails:. chasing their origins and evolution. Res Microbiol 2003,154(4): ...
DeCS 2018 - July 31, 2018 version
T3 Phages use Bacteriophage T3 T3 Receptor use Receptors, Thyroid Hormone T3 Receptor associating Factor use Nuclear Receptor ... T3 Phage use Bacteriophage T3 ... T3 Receptors use Receptors, Thyroid Hormone T3 Thyroid Hormone ... T3 Receptor-associating Factor use Nuclear Receptor Co-Repressor 2 ...
Results for 'Primary antibodies > WB' | Abcam: antibodies, proteins,...
DeCS 2018 - July 31, 2018 version
T3 Phages use Bacteriophage T3 T3 Receptor use Receptors, Thyroid Hormone T3 Receptor associating Factor use Nuclear Receptor ... T3 Phage use Bacteriophage T3 ... T3 Receptors use Receptors, Thyroid Hormone T3 Thyroid Hormone ... T3 Receptor-associating Factor use Nuclear Receptor Co-Repressor 2 ...
DeCS 2019 - June 12, 2019 version
T3 Phages use Bacteriophage T3 T3 Receptor use Receptors, Thyroid Hormone T3 Receptor associating Factor use Nuclear Receptor ... T3 Phage use Bacteriophage T3 ... T3 Receptors use Receptors, Thyroid Hormone T3 Thyroid Hormone ... T3 Receptor-associating Factor use Nuclear Receptor Co-Repressor 2 ...
DeCS 2017 - December 21, 2017 version
T3 Phages use Bacteriophage T3 T3 Receptor use Receptors, Thyroid Hormone T3 Receptor associating Factor use Nuclear Receptor ... T3 Phage use Bacteriophage T3 ... T3 Receptors use Receptors, Thyroid Hormone T3 Thyroid Hormone ... T3 Receptor-associating Factor use Nuclear Receptor Co-Repressor 2 ...
2022 Ecuador Immunodiagnostic Analyzers and Reagents--Supplier Shares and Competitive Analysis, Volume and Sales Segment...
Cortisol, Estradiol, FSH, HCG, Gastrin, LH, Progesterone, PTH/IO PTH, Prolactin, T3, T3 Free, T3 Uptake, T4, T4 Free, TBG, ... Bacteriophage, Streptococcus, E.Coli, Others), By Product (Oral Consumption, External Consumption, Surgical Treatment), By ... Cortisol, Estradiol, FSH, HCG, Gastrin, LH, Progesterone, PTH/IO PTH, Prolactin, T3, T3 Free, T3 Uptake, T4, T4 Free, TBG, ... Marketing T3 Tests. Major Companies Developing or. Marketing T4 Tests. Major Companies Developing or. Marketing TSH Tests. ...
DeCS 2017 - July 04, 2017 version
T3 Phages use Bacteriophage T3 T3 Receptor use Receptors, Thyroid Hormone T3 Receptor associating Factor use Nuclear Receptor ... T3 Phage use Bacteriophage T3 ... T3 Receptors use Receptors, Thyroid Hormone T3 Thyroid Hormone ... T3 Receptor-associating Factor use Nuclear Receptor Co-Repressor 2 ...
A Guide to CRISPR-Cas Nucleases | LoganThrasherCollins.com
The Cas12j enzyme, also known as CasΦ, comes from the genomes of huge bacteriophages of the Biggiephage clade.14 This is ... The resulting constructs were respectively named RESCUE.t1 and RESCUE.t3 and were shown to facilitate conversion of cytosine to ... The resulting constructs were respectively named REPAIR.t1 and REPAIR.t3 and were shown to facilitate adenosine to inosine ... It has been hypothesized that Biggiephages use Cas12j to cut the DNA of other competing bacteriophages. There exist subtypes of ...
SciELO - Brazil - On the use of a probiotic (Bacillus subtilis - strain DSM 17299) as growth promoter in broiler diets On the...
Alternatives to Antibiotics: Utilization of bacteriophage to treat colibacilosis and Prevent foodborne pathogens. Poultry ... T3 Negative Control + Bacillus subtilis (3 x 105 CFUs/ g de feed) and T4 Positive Control (avilamycin + anticoccidial from 1 to ... T3 Negative Control + Bacillus subtilis (3 x 105 CFUs/g feed) and T4 Positive Control (avilamycin + anticoccidial from 1 to 35 ... T3 - Negative Control + Bacillus subtilis (3 x 10(5) CFUs/ g de feed) and T4 - Positive Control (avilamycin + anticoccidial ...
Accession Description Classification Genome Length(bp) molGC
Bacteriophage T5-like cott162 121986 39.744 MF431739 Bacteriophage T5-like chee158 121986 39.746 MF431738 Bacteriophage T5-like ... 003298 Enterobacteria phage T3 38208 49.901 NC_003085 Myxococcus phage Mx8 49534 67.745 NC_002796 Lactococcus phage BK5-T 40003 ... Bacteriophage T5-like poul124 120629 39.264 MF431734 Bacteriophage T5-like saus111K 120620 39.263 MF431733 Bacteriophage T5- ... MF431732 Bacteriophage T5-like pork29 120622 39.263 MF431731 Bacteriophage T5-like pork27 120618 39.264 MF431730 Bacteriophage ...
MUC1 expression and anti-MUC1 serum immune response in head and neck squamous cell carcinoma (HNSCC): a multivariate analysis |...
The immunotherapy nivolumab after surgery helped reduce cancer recurrence in patients with urothelial cancer of the bladder -...
In T2a or T2b, the cancer has invaded the inner or the outer detrusor muscle, and at T3, the tumor has invaded beyond the ... Next articleResearchers have successfully used bacteriophages to treat an antibiotic-resistant mycobacterial lung infection ... After penetrating the muscle and reaching the fatty tissue, the T3 stage is reached, where T4 is characterized as growth of the ...
Find Research outputs
- Yonsei University
MRNA1
- These results suggest that it is the RNA-binding ability of Rho rather than its transcription termination function that is important for the inhibition of bacteriophage growth and the shorter bulk mRNA lifetime. (eurekamag.com)
Phage5
- To broaden our knowledge of the mitochondrial transcriptional apparatus, we have used a polymerase chain reaction (PCR) approach designed to amplify an internal portion of phage T3/T7-like RNA polymerase genes. (omicsdi.org)
- Using this strategy, we have recovered sequences homologous to yeast mitochondrial and phage T3/T7 RNA polymerases from a phylogenetically broad range of multicellular and unicellular eukaryotes. (omicsdi.org)
- We infer that the T3/T7-like RNA polymerase sequences reported here are likely derived from genes encoding the mitochondrial RNA polymerase in the organisms in which they occur, suggesting a phage T3/T7-like RNA polymerase was recruited to act in transcription in the mitochondrion at an early stage in the evolution of this organelle. (omicsdi.org)
- A T3 and T7 recombinant phage acquires efficient adsorption and a broader host range. (omicsdi.org)
- It is usually thought that bacteriophage T7 is female specific, while phage T3 can propagate on male and female Escherichia coli. (omicsdi.org)
Bacillus1
- T3 - Negative Control + Bacillus subtilis (3 x 10(5) CFUs/ g de feed) and T4 - Positive Control (avilamycin + anticoccidial from 1 to 35 days of age). (scielo.br)
Bacterial2
- A total of 120 of 54-week-old Lohman Brown Classic laying hens were subjected to four dietary treatments: control group with no Se supplementation (T1), 0.3 mg/kg of sodium selenite (T2), 0.3 mg/kg of selenium yeast (T3), and 0.3 mg/kg of bacterial Se (Stenotrophomonas maltophilia, ADS18) (T4). (bvsalud.org)
- Bacteriophages-viruses that infect bacterial cells-are the most abundant biological entities on Earth. (cn1699.cn)
Yeast2
- Sequences homologous to yeast mitochondrial and bacteriophage T3 and T7 RNA polymerases are widespread throughout the eukaryotic lineage. (omicsdi.org)
- Although mitochondria and chloroplasts are considered to be descendants of eubacteria-like endo- symbionts, the mitochondrial RNA polymerase of yeast is a nucleus-encoded, single-subunit enzyme homologous to bacteriophage T3 and T7 RNA polymerases, rather than a multi-component, eubacterial-type alpha 2 beta beta' enzyme, as encoded in chloroplast DNA. (omicsdi.org)
Growth2
- We found that the growth patterns of phages T7M and T3 do not match the above characteristics, instead showing strain dependent male exclusion. (omicsdi.org)
- Mutants in Escherichia coli transcription termination factor Rho, termed rho(nusD), were previously isolated based on their ability to block the growth of bacteriophage T4. (eurekamag.com)
Internal3
- Evaluation of the role of bacteriophage against Salmonella Enteritidis (SE) colonization of internal organs (ceca, liver/gall bladder, spleen and ovaries) and the effect of ileal immune response in laying hens was studied. (usda.gov)
- Results suggest that bacteriophage can be used as a dietary strategy to reduce the presence of SE in internal organs and also significantly increased the levels of interferon and interleukin in the ileum. (usda.gov)
- A study was conducted to evaluate the role of bacteriophage (BP) against Salmonella enterica serovar Enteritidis (SE) internal organs colonization and ileum immune response in laying hens. (usda.gov)
Control1
- This functionally diverse protein superfamily regulates the transcription of genes that are involved in the uptake of metals, amino-acid biosynthesis, cell division, the control of plasmid copy number, the lytic cycle of bacteriophages and, perhaps, many other cellular processes. (janelia.org)