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).
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.
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.
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.
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.
Bacteriophage phi 6
Bacteriophage phi X 174
Databases, Nucleic Acid
Influenza A Virus, H3N8 Subtype
Influenza A virus
The type species of the genus INFLUENZAVIRUS A that causes influenza and other diseases in humans and animals. Antigenic variation occurs frequently between strains, allowing classification into subtypes and variants. Transmission is usually by aerosol (human and most non-aquatic hosts) or waterborne (ducks). Infected birds shed the virus in their saliva, nasal secretions, and feces.
Myxovirus Resistance Proteins
Influenza A Virus, H1N1 Subtype
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
RNA Polymerase II
Journal Impact Factor
N4 RNA polymerase II, a heterodimeric RNA polymerase with homology to the single-subunit family of RNA polymerases. (1/14)Bacteriophage N4 middle genes are transcribed by a phage-coded, heterodimeric, rifampin-resistant RNA polymerase, N4 RNA polymerase II (N4 RNAPII). Sequencing and transcriptional analysis revealed that the genes encoding the two subunits comprising N4 RNAPII are translated from a common transcript initiating at the N4 early promoter Pe3. These genes code for proteins of 269 and 404 amino acid residues with sequence similarity to the single-subunit, phage-like RNA polymerases. The genes encoding the N4 RNAPII subunits, as well as a synthetic construct encoding a fusion polypeptide, have been cloned and expressed. Both the individually expressed subunits and the fusion polypeptide reconstitute functional enzymes in vivo and in vitro. (+info)
The phage N4 virion RNA polymerase catalytic domain is related to single-subunit RNA polymerases. (2/14)In vitro, bacteriophage N4 virion RNA polymerase (vRNAP) recognizes in vivo sites of transcription initiation on single-stranded templates. N4 vRNAP promoters are comprised of a hairpin structure and conserved sequences. Here, we show that vRNAP consists of a single 3500 amino acid polypeptide, and we define and characterize a transcriptionally active 1106 amino acid domain (mini-vRNAP). Biochemical and genetic characterization of this domain indicates that, despite its peculiar promoter specificity and lack of extensive sequence similarity to other DNA-dependent RNA polymerases, mini-vRNAP is related to the family of T7-like RNA polymerases. (+info)
Escherichia coli single-stranded DNA-binding protein mediates template recycling during transcription by bacteriophage N4 virion RNA polymerase. (3/14)Coliphage N4 virion RNA polymerase (vRNAP), the most distantly related member of the T7-like family of RNA polymerases, is responsible for transcription of the early genes of the linear double-stranded DNA phage genome. Escherichia coli single-stranded DNA-binding protein (EcoSSB) is required for N4 early transcription in vivo, as well as for in vitro transcription on super-coiled DNA templates containing vRNAP promoters. In contrast to other DNA-dependent RNA polymerases, vRNAP initiates transcription on single-stranded, promoter-containing templates with in vivo specificity; however, the RNA product is not displaced, thus limiting template usage to one round. We show that EcoSSB activates vRNAP transcription at limiting single-stranded template concentrations through template recycling. EcoSSB binds to the template and to the nascent transcript and prevents the formation of a transcriptionally inert RNA:DNA hybrid. Using C-terminally truncated EcoSSB mutant proteins, human mitochondrial SSB (Hsmt SSB), phage P1 SSB, and F episome-encoded SSB, as well as a Hsmt-EcoSSB chimera, we have mapped a determinant of template recycling to the C-terminal amino acids of EcoSSB. T7 RNAP contains an amino-terminal domain responsible for binding the RNA product as it exits from the enzyme. No sequence similarity to this domain exists in vRNAP. Hereby, we propose a unique role for EcoSSB: It functionally substitutes in N4 vRNAP for the N-terminal domain of T7 RNAP responsible for RNA binding. (+info)
Phage N4 RNA polymerase II recruitment to DNA by a single-stranded DNA-binding protein. (4/14)Transcription of bacteriophage N4 middle genes is carried out by a phage-coded, heterodimeric RNA polymerase (N4 RNAPII), which belongs to the family of T7-like RNA polymerases. In contrast to phage T7-RNAP, N4 RNAPII displays no activity on double-stranded templates and low activity on single-stranded templates. In vivo, at least one additional N4-coded protein (p17) is required for N4 middle transcription. We show that N4 ORF2 encodes p17 (gp2). Characterization of purified gp2revealed that it is a single-stranded DNA-binding protein that activates N4 RNAPII transcription on single-stranded DNA templates through specific interaction with N4 RNAPII. On the basis of the properties of the proteins involved in N4 RNAPII transcription and of middle promoters, we propose a model for N4 RNAPII promoter recognition, in which gp2plays two roles, stabilization of a single-stranded region at the promoter and recruitment of N4 RNAPII through gp2-N4 RNAPII interactions. Furthermore, we discuss our results in the context of transcription initiation by mitochondrial RNA polymerases. (+info)
Bacteriophage N4 virion RNA polymerase interaction with its promoter DNA hairpin. (5/14)Bacteriophage N4 minivirion RNA polymerase (mini-vRNAP), the RNA polymerase (RNAP) domain of vRNAP, is a member of the T7-like RNAP family. Mini-vRNAP recognizes promoters that comprise conserved sequences and a 3-base loop-5-base pair (bp) stem DNA hairpin structure on single-stranded templates. Here, we defined the DNA structural and sequence requirements for mini-vRNAP promoter recognition. Mini-vRNAP binds a 20-nucleotide (nt) N4 P2 promoter deoxyoligonucleotide with high affinity (K(d) = 2 nM) to form a salt-resistant complex. We show that mini-vRNAP interacts specifically with the central base of the hairpin loop (-11G) and a base at the stem (-8G) and that the guanine 6-keto and 7-imino groups at both positions are essential for binding and complex salt resistance. The major determinant (-11G), which must be presented to mini-vRNAP in the context of a hairpin loop, appears to interact with mini-vRNAP Trp-129. This interaction requires template single-strandedness at positions -2 and -1. Contacts with the promoter are disrupted when the RNA product becomes 11-12 nt long. This detailed description of vRNAP interaction with its promoter hairpin provides insights into RNAP-promoter interactions and explains how the injected vRNAP, which is present in one or two copies, recognizes its promoters on a single copy of the injected genome. (+info)
X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase. (6/14)(+info)
Insight into DNA and protein transport in double-stranded DNA viruses: the structure of bacteriophage N4. (7/14)(+info)
The tail sheath of bacteriophage N4 interacts with the Escherichia coli receptor. (8/14)(+info)
Phage - definition of phage by The Free Dictionary
Define phage. phage synonyms, phage pronunciation, phage translation, English dictionary definition of phage. n. A bacteriophage. n short for bacteriophage n. bacteriophage. a combining form meaning
A scalable pipeline for highly effective genetic modification of a malaria parasite<...
TY - JOUR. T1 - A scalable pipeline for highly effective genetic modification of a malaria parasite. AU - Pfander, Claudia. AU - Anar, Burcu. AU - Schwach, Frank. AU - Otto, Thomas D.. AU - Brochet, Mathieu. AU - Volkmann, Katrin. AU - Quail, Michael A.. AU - Pain, Arnab. AU - Rosen, Barry. AU - Skarnes, William. AU - Rayner, Julian C.. AU - Billker, Oliver. N1 - KAUST Repository Item: Exported on 2020-10-01. PY - 2011/10/23. Y1 - 2011/10/23. N2 - In malaria parasites, the systematic experimental validation of drug and vaccine targets by reverse genetics is constrained by the inefficiency of homologous recombination and by the difficulty of manipulating adenine and thymine (A+T)-rich DNA of most Plasmodium species in Escherichia coli. We overcame these roadblocks by creating a high-integrity library of Plasmodium berghei genomic DNA (,77% A+T content) in a bacteriophage N15-based vector that can be modified efficiently using the lambda Red method of recombineering. We built a pipeline for ...
Reactome | Pre-snRNA transcript initiation, Integrator binding, LEC binding
Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.
5121 Telomeres, centromeres, and other highly repetitive genomic regions are typically under-represented in shotgun libraries, and they are often absent from partial-digest BAC libraries. Accurate cloning of isolated fragments containing short tandem repeats, AT-rich DNA, or regions with strong secondary structure likewise can be difficult or impossible using conventional supercoiled plasmids. We have developed vectors and methods to alleviate these types of cloning bias. A transcription-free, linear plasmid was derived from the linear coliphage N15 for cloning into E.coli. The ends of the vector are free to rotate during replication, minimizing formation of secondary structures that are substrates for deletion or rearrangement. The pJAZZ linear vectors are shown to provide unprecedented ability to maintain regions of up to 30 kb that are unclonable in circular plasmids. Examples include regions of di-, tri-, and tetra-nucleotide repeats up to several kb, as well as highly AT-rich fragments of ...
Hatfull, G.F. and Sarkis, G.J. (1993). DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics. Mol. Microbiol., 7, 395-405.. Hatfull, G.F., Cresawn, S.G. and Hendrix, R.W. (2008). Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution Res. Microbiol., 159, 332-339.. Lubbers, M.W., Waterfield, N.R., Beresford, T.P.J., Le Page, R.W.F. and Jarvis, A.W. (1995). Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes. Appl. Environ. Microbiol., 61, 4348-4356.. Ravin, V., Ravin, N., Casjens, S., Ford, M., Hatfull, G. and Hendrix, R. (2000). Genomic sequence and analysis of the atypical temperate bacteriophage N15. J. Mol. Biol., 299, 53-73.. Robert, M.D., Martin, N.L. and Kropinski, A.M. (2004). The genome and proteome of coliphage T1. Virology, 318, 245-266.. Schouler, C., Ehrlich, S.D. and Chopin, M.-C. (1994). Sequence and organization of the ...
N15likevirus - Wikipedia
N15likevirus (synonym N15-like viruses) is a genus of viruses in the order Caudovirales, in the family Siphoviridae. Bacteria serve as natural hosts, with transmission achieved through passive diffusion. There is currently only one species in this genus: the type species Enterobacteria phage N15. Group: dsDNA Order: Caudovirales Family: Siphoviridae Genus: N15likevirus Enterobacteria phage N15 N15likeviruses are nonenveloped, with a head and tail. The head is about 60 nm in diameter. The tail is long and flexible, at about 140 nm long, 8 nm wide, with short brush-like terminal fibers. Enterobacteria phage N15 has been fully sequenced. It has about 46k nucleotides, with 60 proteins. The complete genome is available here Viral replication is cytoplasmic. The virus attaches to the host cells adhesion receptors using its terminal fiber, and ejects the viral DNA into the host cytoplasm via long flexible tail ejection system. Replication follows the replicative transposition model. DNA-templated ...
Branch Detailed Info | Queens Library
In 1869, New York attorney Albon Platt Man purchased the Lefferts and Wellings Farms in West Jamaica, an area settled before the Revolutionary War. Envisioning a garden spot and refuge from city life in Manhattan, he recruited landscape architect Edward Richmond to help lay out his proposed community. It was one of the citys first planned garden communities. All streets were well laid out with trees planted on both sides. When Edward Richmond died in 1870, real estate developer, Oliver Fowler, became Mans partner. Lefferts Avenue, now Lefferts Boulevard, became the main thoroughfare.. Man called this new community Richmond Hill. Richmond Hill was also the name given to the 138 foot hill located north of Metropolitan Avenue on 116th Street. The name is believed to come from the London suburb of Richmond Hill, although some sources claim that it was named after Edward Richmond, the developer. Kew Gardens, originally North Richmond Hill, was established later in 1912. It was named after the ...
PAFAH2 - Wikipedia
Platelet-activating factor acetylhydrolase 2, cytoplasmic is an enzyme that in humans is encoded by the PAFAH2 gene. It is one of several PAF acetylhydrolases. This gene encodes platelet-activating factor acetylhydrolase isoform 2, a single-subunit intracellular enzyme that catalyzes the removal of the acetyl group at the SN-2 position of platelet-activating factor (identified as 1-O-alkyl-2-acetyl-sn-glyceryl-3-phosphorylcholine). However, this lipase exhibits a broader substrate specificity than simply platelet activating factor. Two other isoforms of intracellular platelet-activating factor acetylhydrolase exist, and both are multi-subunit enzymes. Additionally, there is a single-subunit serum isoform of this enzyme. GRCh38: Ensembl release 89: ENSG00000158006 - Ensembl, May 2017 GRCm38: Ensembl release 89: ENSMUSG00000037366 - Ensembl, May 2017 Human PubMed Reference:. Mouse PubMed Reference:. Hattori K, Adachi H, Matsuzawa A, Yamamoto K, Tsujimoto M, Aoki J, Hattori M, Arai H, Inoue K ...
Azorhizobium caulinodans nfrA protein Summary Report | CureHunter
Azorhizobium caulinodans nfrA protein: RNA-binding protein that stimulates the elongation of poly(A) tails; may be involved in the regulation of nifA; homologous to HF-I protein of Escherichia coli; Do Not confuse with nrfA, a cytochrome c nitrite reductase (EC 220.127.116.11); DO NOT confuse with NfrA protein of E. coli, a bacteriophage N4 adsorption protein; amino acid sequence given in first source; GenBank X76450
A novel intermediate in transcription initiation by human mitochondrial RNA polymerase
The mitochondrial genome is transcribed by a single-subunit T7 phage-like RNA polymerase (mtRNAP), structurally unrelated to cellular RNAPs. In higher eukaryotes, mtRNAP requires two transcription factors for efficient initiation-TFAM, a major nucleoid protein, and TFB2M, a transient component of mt …
Nucleotidyl | definition of nucleotidyl by Medical dictionary
Looking for online definition of nucleotidyl in the Medical Dictionary? nucleotidyl explanation free. What is nucleotidyl? Meaning of nucleotidyl medical term. What does nucleotidyl mean?
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Nitasha Menon | Profiles RNS
C6 H15 N4 O2 1 175.209 ASN L-peptide linking y ASPARAGINE ? C4 H8 N2 O3 132.118 ASP L-peptide linking y ASPARTIC ACID ... P1 PROTEIN FROM BACTERIOPHAGE PHI6 # _entity_poly.entity_id 1 _entity_poly.type polypeptide(L) _entity_poly.nstd_linkage no ... BACTERIOPHAGE PHI6 POLYMERASE COMPLEX ASSEMBLED IN VITRO FROM PURIFIED PROTEINS P1, P2, AND P4 _em_entity_assembly.type ... STRUCTURE OF THE P2 POLYMERASE INSIDE IN VITRO ASSEMBLED BACTERIOPHAGE PHI6 POLYMERASE COMPLEX, WITH P1 INCLUDED EMDB EMD-3185 ...