https://ecoliwiki.org/colipedia/api.php?action=feedcontributions&feedformat=atom&user=46.161.41.24EcoliWiki - User contributions [en]2026-11-05T16:07:45ZUser contributionsMediaWiki 1.43.11https://ecoliwiki.org/colipedia/index.php?title=PMID:2383568&diff=1490906PMID:23835682014-03-26T19:35:29Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Bamford, DH, Bamford, JK, Towse, SA and Thomas, GJ Jr''' (1990) Structural study of the lipid-containing bacteriophage PRD1 and its capsid and DNA components by laser Raman spectroscopy. ''Biochemistry'' '''29''':5982-7<br />
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The Raman spectrum of a virus contains the structural signature of each of its molecular components (Thomas, 1987). We report the first Raman spectrum obtained from an intact, lipid-containing virus--the icosahedral bacteriophage PRD1--and show that this spectrum contains characteristic structure markers for the major capsid protein, the packaged double-stranded DNA genome, and the viral membrane which resides between the capsid and DNA. We find that the packaged genome of PRD1 exhibits Raman markers typical of the B-DNA secondary structure. Comparison of the Raman spectrum of the packaged DNA with that of protein-free DNA extracted from the virion shows further that the B-form secondary structure is not significantly perturbed by packaging in the virion. The Raman signature of the PRD1 membrane, monitored within the virion at 4 degrees C, is that of a phospholipid liquid-crystalline phase. The PRD1 capsid, which comprises several hundred copies of the major coat protein P3 (product of viral gene III) and a few copies of minor proteins, incorporates P3 capsomers predominantly in the beta-sheet conformation. The beta-sheet structure of P3 is maintained in the fully assembled PRD1 virion, as well as in the empty capsid. The present results demonstrate the feasibility of obtaining structural information from the three different classes of biomolecules--nucleic acid, protein, and lipid--which constitute a membrane-lined virus particle. Our results also demonstrate that the coat protein and double-stranded DNA components of a lipid-containing bacteriophage share many structural features in common with bacteriophage lacking a lipid membrane.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2383568 PubMed]<br />
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Bacteriophages/ultrastructure; Capsid; Chemistry, Physical; DNA, Viral; Lasers; Lipids; Nucleic Acid Conformation; Physicochemical Phenomena; Protein Conformation; Spectrum Analysis, Raman/methods<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:2383568&diff=1490905PMID:23835682014-03-26T19:35:28Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:8557027&diff=1490898PMID:85570272014-03-24T16:09:21Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Butcher, SJ, Bamford, DH and Fuller, SD''' (1995) DNA packaging orders the membrane of bacteriophage PRD1. ''EMBO J.'' '''14''':6078-86<br />
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Bacteriophage PRD1 contains a linear dsDNA genome enclosed by a lipid membrane lying within a protein coat. Determination of the structure of the detergent-treated particle to 2 nm by cryo-electron microscopy and three-dimensional reconstruction has defined the position of the major coat protein P3. The coat contains 240 copies of trimeric P3 packed into positions of local 6-fold symmetry on a T = 25 lattice. The three-dimensional structures of the PRD1 virion and a DNA packaging mutant to a resolution of 2.8 nm have revealed specific interactions between the coat and the underlying membrane. The membrane is clearly visible as two leaflets separated by 2 nm and spanned by transmembrane density. The size of the coat does not change upon DNA packaging. Instead, the number of interactions seen between the protein shell and the membrane and the order of the membrane components increase. Thus the membrane of PRD1 plays a role in assembly which is akin to that played by the nucleocapsid in other membrane viruses.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8557027 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394732 PMC394732]<br />
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Bacteriophages/chemistry; Bacteriophages/growth & development; Bacteriophages/ultrastructure; Capsid/chemistry; Capsid/ultrastructure; Capsid Proteins; DNA, Viral/chemistry; DNA, Viral/ultrastructure; Image Processing, Computer-Assisted; Microscopy, Electron; Models, Molecular; Protein Conformation<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:8557027&diff=1490897PMID:85570272014-03-24T16:09:20Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:10448038&diff=1490695PMID:104480382013-12-30T07:05:22Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Rydman, PS, Caldentey, J, Butcher, SJ, Fuller, SD, Rutten, T and Bamford, DH''' (1999) Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex. ''J. Mol. Biol.'' '''291''':575-87<br />
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Bacteriophage PRD1 is a membrane-containing virus with an unexpected similarity to adenovirus. We mutagenized unassigned PRD1 genes to identify minor capsid proteins that could be structural or functional analogs to adenovirus proteins. We report here the identification of an amber mutant, sus525, in an essential PRD1 gene XXXI. The gene was cloned and the gene product was overexpressed and purified to near homogeneity. Analytical ultracentrifugation and gel filtration showed that P31 is a homopentamer of about 70 kDa. The protein was shown to be accessible on the virion surface and its absence in the sus525 particles led to the deficiency of two other viral coat proteins, protein P5 and the adsorption protein P2. Cryo-electron microscopy and image reconstruction of the sus525 particles indicate that these proteins are located on the capsid vertices, because in these particles the entire vertex structure was missing along with the peripentonal major capsid protein P3 trimers. Sus525 particles package DNA effectively but loose it upon purification. All of the PRD1 vertex structures are labile and potentially capable of mediating DNA delivery; this is in contrast to other dsDNA phages which employ a single vertex for packaging and delivery. We propose that this arises from a symmetry mismatch between protein P2 and the pentameric P31 in analogy to that between the adenovirus penton base and the receptor-binding spike.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10448038 PubMed]<br />
Online version:[http://dx.doi.org/10.1006/jmbi.1999.2978 10.1006/jmbi.1999.2978]<br />
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Adenoviridae/chemistry; Adenoviridae/genetics; Adenoviridae/ultrastructure; Binding Sites; Capsid/chemistry; Capsid/genetics; Capsid/ultrastructure; DNA, Viral/chemistry; Genes, Viral; Microscopy, Electron; Molecular Weight; Mutation; Protein Conformation; Recombinant Proteins/chemistry; Recombinant Proteins/genetics; Recombinant Proteins/ultrastructure; Species Specificity; Tectiviridae/chemistry; Tectiviridae/genetics; Tectiviridae/ultrastructure<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:10448038&diff=1490694PMID:104480382013-12-30T07:03:20Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:8331725&diff=1490689PMID:83317252013-12-26T21:08:03Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Savilahti, H and Bamford, DH''' (1993) Protein-primed DNA replication: role of inverted terminal repeats in the Escherichia coli bacteriophage PRD1 life cycle. ''J. Virol.'' '''67''':4696-703<br />
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Escherichia coli bacteriophage PRD1 and its relatives contain linear double-stranded DNA genomes, the replication of which proceeds via a protein-primed mechanism. Characteristically, these molecules contain 5'-covalently bound terminal proteins and inverted terminal nucleotide sequences (inverted terminal repeats [ITRs]). The ITRs of each PRD1 phage species have evolved in parallel, suggesting communication between the molecule ends during the life cycle of these viruses. This process was studied by constructing chimeric PRD1 phage DNA molecules with dissimilar end sequences. These molecules were created by combining two closely related phage genomes (i) in vivo by homologous recombination and (ii) in vitro by ligation of appropriate DNA restriction fragments. The fate of the ITRs after propagation of single genomes was monitored by DNA sequence analysis. Recombinants created in vivo showed that phages with nonidentical genome termini are viable and relatively stable, and hybrid phages made in vitro verified this observation. However, genomes in which the dissimilar DNA termini had regained identical sequences were also detected. These observations are explained by a DNA replication model involving two not mutually exclusive pathways. The generality of this model in protein-primed DNA replication is discussed.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8331725 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC237855 PMC237855]<br />
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Amino Acid Sequence; Base Sequence; Coliphages/genetics; Coliphages/metabolism; Coliphages/physiology; Conserved Sequence; DNA Replication; DNA, Viral/genetics; DNA, Viral/isolation & purification; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli/physiology; Genome, Viral; Models, Genetic; Models, Structural; Molecular Sequence Data; Repetitive Sequences, Nucleic Acid; Salmonella typhimurium/genetics; Sequence Homology, Nucleic Acid<br />
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{{LitMaterials}}<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:8331725&diff=1490688PMID:83317252013-12-26T21:08:02Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:6757459&diff=1490687PMID:67574592013-12-26T13:18:03Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Mindich, L, Bamford, D, Goldthwaite, C, Laverty, M and Mackenzie, G''' (1982) Isolation of nonsense mutants of lipid-containing bacteriophage PRD1. ''J. Virol.'' '''44''':1013-20<br />
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We isolated nonsense mutants of bacteriophage PRD1, a lipid-containing polyhedral virus capable of infecting many genera of gram-negative bacteria. These mutants were grouped into 19 classes on the basis of genetic complementation and sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis. PRD1 infection led to the synthesis of at least 25 viral proteins, 17 of which were components of mature virions. The synthesis of proteins fell into the following three classes: very early, middle early, and late. Two of the very early proteins, P1 and P8, had an effect on DNA synthesis, host protein synthesis shutoff, and the turning on of middle and late protein synthesis. Another very early protein, P12, was involved in the shutoff of early protein synthesis. Two genes were identified as affecting lysis of the host. One appeared to be a lysin, whereas the other was an accessory lytic factor.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6757459 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC256361 PMC256361]<br />
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Genetic Complementation Test; Lipids/analysis; Molecular Weight; Mutation; Plasmids; Recombination, Genetic; Salmonella Phages/genetics; Salmonella typhimurium/genetics; Viral Proteins/genetics; Viral Proteins/isolation & purification<br />
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{{LitSignificance}}<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:6757459&diff=1490686PMID:67574592013-12-26T13:18:03Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:1853567&diff=1490685PMID:18535672013-12-26T08:01:38Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Bamford, JK, Hänninen, AL, Pakula, TM, Ojala, PM, Kalkkinen, N, Frilander, M and Bamford, DH''' (1991) Genome organization of membrane-containing bacteriophage PRD1. ''Virology'' '''183''':658-76<br />
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We have determined the nucleotide sequence of the late region (11 kbp) of the lipid-containing bacteriophage PRD1. Gene localization was carried out by complementing nonsense phage mutants with genomic clones containing specific reading frames. The localization was confirmed by sequencing the N-termini of isolated gene products as well as sequencing the N-termini of tryptic fragments of the phage membrane-associated proteins. This, with the previously obtained sequence of the early regions, allowed us to organize most of the phage genes in the phage genome.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1853567 PubMed]<br />
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Amino Acid Sequence; Bacteriophages/genetics; Base Sequence; Cloning, Molecular; DNA, Viral; Electrophoresis, Polyacrylamide Gel; Genes, Viral; Genetic Complementation Test; Gram-Negative Bacteria; Molecular Sequence Data; Mutation; Open Reading Frames; Restriction Mapping; Viral Envelope Proteins/genetics<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
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== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
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<annotationlinks/><br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:1853567&diff=1490684PMID:18535672013-12-26T08:01:37Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:11741849&diff=1490683PMID:117418492013-12-25T20:51:23Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Rydman, PS and Bamford, DH''' (2002) The lytic enzyme of bacteriophage PRD1 is associated with the viral membrane. ''J. Bacteriol.'' '''184''':104-10<br />
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Bacteriophage PRD1 encodes two proteins (P7 and P15) that are associated with a muralytic activity. Protein P15 is a soluble beta-1,4-N-acetylmuramidase that causes phage-induced host cell lysis. We demonstrate here that P15 is also a structural component of the PRD1 virion and that it is connected to the phage membrane. Small viral membrane proteins P20 and P22 modulate incorporation of P15 into the virion and may connect it to the phage membrane. The principal muralytic protein involved in PRD1 DNA entry seems to be the putative lytic transglycosylase protein P7, as the absence of protein P15 did not delay initiation of phage DNA replication in the virus-host system used. The incorporation of two different lytic enzymes into virions may reflect the broad host range of bacteriophage PRD1.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11741849 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC134774 PMC134774]<br />
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Bacteriolysis; Bacteriophage PRD1/enzymology; Bacteriophage PRD1/growth & development; DNA Replication; Glycoside Hydrolases/isolation & purification; Glycoside Hydrolases/metabolism; Gram-Negative Bacteria/virology; Muramidase/isolation & purification; Muramidase/metabolism; Viral Matrix Proteins/isolation & purification; Viral Matrix Proteins/metabolism; Viral Proteins<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:11741849&diff=1490682PMID:117418492013-12-25T20:51:23Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:2196741&diff=1490681PMID:21967412013-12-25T12:25:45Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Bamford, JK and Bamford, DH''' (1990) Capsomer proteins of bacteriophage PRD1, a bacterial virus with a membrane. ''Virology'' '''177''':445-51<br />
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Bacteriophage PRD1 infecting Escherichia coli and Salmonella typhimurium translocates its membrane from the host plasma membrane to the virus particle. One obligatory component in this process is the major capsid protein. In this investigation we describe characteristics of the homomultimeric major and minor capsid proteins including the sequences of the corresponding genes. The minor capsid protein was found to contain a short collagen-like region (Gly-X-Y)6. This is the first time this motif has been reported for a prokaryotic protein.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2196741 PubMed]<br />
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|-<br />
!align=left |Keywords<br />
||<br />
Amino Acid Sequence; Bacteriophages/genetics; Bacteriophages/isolation & purification; Base Sequence; Capsid/genetics; DNA, Viral/genetics; DNA, Viral/isolation & purification; Electrophoresis, Polyacrylamide Gel; Escherichia coli/genetics; Genes, Viral; Molecular Sequence Data; Molecular Weight; Mutation; Protein Conformation; Salmonella typhimurium/genetics; Viral Structural Proteins/genetics<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:2196741&diff=1490680PMID:21967412013-12-25T12:25:44Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:2023249&diff=1490679PMID:20232492013-12-25T07:55:26Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Yoo, SK and Ito, J''' (1991) Sequence requirements for protein-primed DNA replication of bacteriophage PRD1. ''J. Mol. Biol.'' '''218''':779-89<br />
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In vitro studies have demonstrated that linear duplex, protein-free DNA molecules containing an inverted terminal repeat (ITR) sequence of the PRD1 genome at one end can undergo replication by a protein-primed mechanism. No DNA replication was observed when the ITR sequence was deleted or was not exposed at the terminus of the template DNA. We have determined the minimal origin of replication by analyzing the template activity of various deletion derivatives. Our results showed that the terminal 20 base-pairs of ITR are required for efficient in vitro DNA replication. We have found that, within the minimal replication origin region, there are complementary sequences. A site-specific mutagenesis analysis showed that most of the point mutations in the complementary sequences markedly reduced the template activity. The analyses of the results obtained with synthetic oligonucleotides have revealed that the specificity of the replication origin is strand specific and even on a single-stranded template a particular DNA sequence including a 3'-terminal C residue is required for the initiation of PRD1 DNA replication in vitro.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2023249 PubMed]<br />
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Bacteriophages/genetics; Base Sequence; DNA Replication; DNA, Viral/biosynthesis; Molecular Sequence Data; Mutagenesis, Site-Directed; Oligonucleotides; Plasmids; Polymerase Chain Reaction; Templates, Genetic<br />
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{{LitSignificance}}<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:2023249&diff=1490678PMID:20232492013-12-25T07:55:26Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:7793328&diff=1490677PMID:77933282013-12-24T15:28:58Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Bamford, DH, Caldentey, J and Bamford, JK''' (1995) Bacteriophage PRD1: a broad host range DSDNA tectivirus with an internal membrane. ''Adv. Virus Res.'' '''45''':281-319<br />
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No abstract in PubMed<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7793328 PubMed]<br />
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Base Sequence; DNA Replication; DNA, Viral/biosynthesis; Genome, Viral; Molecular Sequence Data; Tectiviridae/genetics; Tectiviridae/physiology; Virion; Virus Replication<br />
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{{LitMaterials}}<br />
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{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:7793328&diff=1490676PMID:77933282013-12-24T15:28:58Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:4211861&diff=1490675PMID:42118612013-12-24T13:25:47Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Olsen, RH, Siak, JS and Gray, RH''' (1974) Characteristics of PRD1, a plasmid-dependent broad host range DNA bacteriophage. ''J. Virol.'' '''14''':689-99<br />
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||<br />
Several distinctive properties of PRD1, an icosahedral plasmid-dependent phage, are described. The drug-resistance plasmid-dependent host range of PRD1 extends beyond the P incompatibility group and includes gram-negative bacteria containing plasmids of incompatibility groups N and W. PRD1 phage will infect pseudomonads and Enterobacteriaceae containing either a P or W incompatibility group plasmid. PRD1 adsorbs to the cell wall of R(+) bacteria and thus its infectivity indicates cell wall alterations by these drug-resistance plasmid groups. PRD1 nucleic acid is duplex DNA with an estimated molecular weight of 24 x 10(6). The appearance of PRD1 in electron micrographs is suggestive of lipid content in addition to its buoyant density of 1.348 in CsCl and its sensitivity to chloroform. The latent period of PRD1 varies with the R(+) host bacterial strain used for growth of the phage.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=4211861 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC355564 PMC355564]<br />
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Adsorption; Alcaligenes; Azotobacter; Bacteriophages/growth & development; Centrifugation, Zonal; DNA, Viral/analysis; Escherichia coli; Extrachromosomal Inheritance; Microscopy, Electron; Molecular Weight; Neisseria; Proteus mirabilis; Pseudomonas aeruginosa; Pseudomonas fluorescens; Salmonella typhimurium; Shigella boydii; Vibrio cholerae; Virus Replication<br />
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<annotationlinks/><br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:4211861&diff=1490674PMID:42118612013-12-24T13:25:46Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:6620455&diff=1490673PMID:66204552013-12-24T03:03:51Z<p>46.161.41.24: Fill PMID: Page!</p>
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||<br />
'''Bamford, D, McGraw, T, MacKenzie, G and Mindich, L''' (1983) Identification of a protein bound to the termini of bacteriophage PRD1 DNA. ''J. Virol.'' '''47''':311-6<br />
|-<br />
!align=left |Abstract<br />
||<br />
Lipid-containing bacteriophage PRD1 has a double-stranded DNA genome of about 14,500 nucleotide base pairs. The phage can infect Escherichia coli and Salmonella typhimurium as well as other gram-negative bacteria harboring an appropriate plasmid. [35S]methionine label is incorporated into the DNA band early in infection. The label remains associated with DNA through phenol extraction and boiling with sodium dodecyl sulfate. Nuclease treatment of the genome released a protein which migrated as an early phage-specific protein (P8). This protein is also necessary for phage DNA replication. By restriction enzyme analysis it was shown that protein was associated with the terminal restriction fragments. Extracts of infected cells catalyzed the labeling of protein P8 with [alpha-32P]dGTP.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6620455 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC255262 PMC255262]<br />
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Bacteriophages/analysis; DNA, Viral/analysis; Electrophoresis, Polyacrylamide Gel; Viral Proteins/analysis<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
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==References==<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:6620455&diff=1490672PMID:66204552013-12-24T03:03:51Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:2251117&diff=1490671PMID:22511172013-12-23T22:35:58Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Pakula, TM, Caldentey, J, Serrano, M, Gutierrez, C, Hermoso, JM, Salas, M and Bamford, DH''' (1990) Characterization of a DNA binding protein of bacteriophage PRD1 involved in DNA replication. ''Nucleic Acids Res.'' '''18''':6553-7<br />
|-<br />
!align=left |Abstract<br />
||<br />
Escherichia coli phage PRD1 protein P12, involved in PRD1 DNA replication in vivo, has been highly purified from E. coli cells harbouring a gene XII-containing plasmid. Protein P12 binds to single-stranded DNA as shown by gel retardation assays and nuclease protection experiments. Binding of protein P12 to single-stranded DNA increases about 14% the contour length of the DNA as revealed by electron microscopy. Binding to single-stranded DNA seems to be cooperative, and it is not sequence specific. Protein P12 also binds to double-stranded DNA although with an affinity 10 times lower than to single-stranded DNA. Using the in vitro phage phi 29 DNA replication system, it is shown that protein P12 stimulates the overall phi 29 DNA replication.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2251117 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC332609 PMC332609]<br />
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||<br />
Coliphages/drug effects; Coliphages/metabolism; DNA/metabolism; DNA Replication/drug effects; DNA, Single-Stranded/metabolism; DNA, Viral/biosynthesis; DNA-Binding Proteins/genetics; Nucleic Acid Conformation; Protein Conformation; Viral Proteins/pharmacology<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:2251117&diff=1490670PMID:22511172013-12-23T22:35:58Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:10956048&diff=1490669PMID:109560482013-12-23T16:00:33Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Caldentey, J, Tuma, R and Bamford, DH''' (2000) Assembly of bacteriophage PRD1 spike complex: role of the multidomain protein P5. ''Biochemistry'' '''39''':10566-73<br />
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!align=left |Abstract<br />
||<br />
The spike structure of bacteriophage PRD1 is comprised of proteins P2, P5, and P31. It resembles the corresponding receptor-binding structure of adenoviruses. We show that purified recombinant protein P5 is an elongated (30 x 2.7 nm; R(h) = 5.5 nm), multidomain trimer which can slowly associate into nonamers. Cleavage of the 340 amino acid long P5 with collagenase yields 2 fragments. The larger, 205 amino acid long C-terminal fragment appears to contain the residues responsible for the trimerization of the protein, whereas the smaller N-terminal part mediates the interaction of P5 with the pentameric vertex protein P31 (24 x 2.5 nm, R(h) = 4.2 nm). In addition, the presence of the N-terminal sequence is required for the formation of the P5 nonamer. The results presented here suggest that P5 and P31 form an elongated adaptor complex at the 5-fold vertexes of the virion which anchors the adsorption protein P2 (21 x 2.5 nm; R(h) = 4.1 nm). Our results also suggest that the P5 trimer forms a substantial part of the viral spike shaft that was previously thought to be composed exclusively of protein P2.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10956048 PubMed]<br />
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!align=left |Keywords<br />
||<br />
Amino Acid Motifs; Amino Acid Sequence; Collagen/chemistry; Collagen/genetics; Kinetics; Macromolecular Substances; Models, Molecular; Molecular Sequence Data; Protein Structure, Quaternary; Protein Structure, Tertiary; Recombinant Proteins/chemistry; Recombinant Proteins/genetics; Recombinant Proteins/metabolism; Sequence Homology, Amino Acid; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Tectiviridae/chemistry; Tectiviridae/genetics; Tectiviridae/metabolism; Viral Proteins/chemistry; Viral Proteins/genetics; Viral Proteins/metabolism<br />
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{{LitSignificance}}<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:10956048&diff=1490668PMID:109560482013-12-23T16:00:32Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:10542170&diff=1490667PMID:105421702013-12-23T10:24:00Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Grahn, AM, Caldentey, J, Bamford, JK and Bamford, DH''' (1999) Stable packaging of phage PRD1 DNA requires adsorption protein P2, which binds to the IncP plasmid-encoded conjugative transfer complex. ''J. Bacteriol.'' '''181''':6689-96<br />
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!align=left |Abstract<br />
||<br />
The double-stranded DNA bacteriophage PRD1 uses an IncP plasmid-encoded conjugal transfer complex as a receptor. Plasmid functions in the PRD1 life cycle are restricted to phage adsorption and DNA entry. A single phage structural protein, P2, located at the fivefold capsid vertices, is responsible for PRD1 attachment to its host. The purified recombinant adsorption protein was judged to be monomeric by gel filtration, rate zonal centrifugation, analytical ultracentrifugation, and chemical cross-linking. It binds to its receptor with an apparent K(d) of 0.20 nM, and this binding prevents phage adsorption. P2-deficient particles are unstable and spontaneously release the DNA with concomitant formation of the tail-like structure originating from the phage membrane. We envisage the DNA to be packaged through one vertex, but the presence of P2 on the other vertices suggests a mechanism whereby the injection vertex is determined by P2 binding to the receptor.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10542170 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC94133 PMC94133]<br />
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Adsorption; Bacteriophages/genetics; Bacteriophages/metabolism; Bacteriophages/physiology; Conjugation, Genetic; DNA, Viral/metabolism; Plasmids/genetics; Receptors, Virus/metabolism; Recombinant Proteins/chemistry; Recombinant Proteins/metabolism; Viral Structural Proteins/chemistry; Viral Structural Proteins/genetics; Viral Structural Proteins/metabolism; Virion/chemistry<br />
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==References==<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:10542170&diff=1490666PMID:105421702013-12-23T10:23:59Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22589288&diff=1490602PMID:225892882013-11-09T20:32:50Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Kendall, MM, Gruber, CC, Parker, CT and Sperandio, V''' (2012) Ethanolamine controls expression of genes encoding components involved in interkingdom signaling and virulence in enterohemorrhagic Escherichia coli O157:H7. ''MBio'' '''3'''<br />
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Bacterial pathogens must be able to both recognize suitable niches within the host for colonization and successfully compete with commensal flora for nutrients in order to establish infection. Ethanolamine (EA) is a major component of mammalian and bacterial membranes and is used by pathogens as a carbon and/or nitrogen source in the gastrointestinal tract. The deadly human pathogen enterohemorrhagic Escherichia coli O157:H7 (EHEC) uses EA in the intestine as a nitrogen source as a competitive advantage for colonization over the microbial flora. Here we show that EA is not only important for nitrogen metabolism but that it is also used as a signaling molecule in cell-to-cell signaling to activate virulence gene expression in EHEC. EA in concentrations that cannot promote growth as a nitrogen source can activate expression of EHEC's repertoire of virulence genes. The EutR transcription factor, known to be the receptor of EA, is only partially responsible for this regulation, suggesting that yet another EA receptor exists. This important link of EA with metabolism, cell-to-cell signaling, and pathogenesis, highlights the fact that a fundamental means of communication within microbial communities relies on energy production and processing of metabolites. Here we show for the first time that bacterial pathogens not only exploit EA as a metabolite but also coopt EA as a signaling molecule to recognize the gastrointestinal environment and promote virulence expression. IMPORTANCE: In order to successfully cause disease, a pathogen must be able to sense a host environment and modulate expression of its virulence genes as well as compete with the indigenous microbiota for nutrients. Ethanolamine (EA) is present in the large intestine due to the turnover of intestinal cells. Here, we show that the human pathogen Escherichia coli O157:H7, which causes bloody diarrhea and hemolytic-uremic syndrome, regulates virulence gene expression through EA metabolism and by responding to EA as a signal. These findings provide the first information directly linking EA with bacterial pathogenesis.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22589288 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972 PMC3372972]<br />
Online version:[http://dx.doi.org/10.1128/mBio.00050-12 10.1128/mBio.00050-12]<br />
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Escherichia coli Infections/metabolism; Escherichia coli Infections/microbiology; Escherichia coli O157/genetics; Escherichia coli O157/metabolism; Escherichia coli O157/pathogenicity; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Ethanolamine/metabolism; Gastrointestinal Tract/metabolism; Gastrointestinal Tract/microbiology; Gene Expression Regulation, Bacterial; Humans; Signal Transduction; Virulence<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22589288&diff=1490601PMID:225892882013-11-09T20:32:49Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:23472115&diff=1490536PMID:234721152013-10-06T14:30:46Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Arunasri, K, Adil, M, Venu Charan, K, Suvro, C, Himabindu Reddy, S and Shivaji, S''' (2013) Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression. ''PLoS ONE'' '''8''':e57860<br />
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||<br />
This study demonstrates the effects of simulated microgravity on E. coli K 12 MG1655 grown on LB medium supplemented with glycerol. Global gene expression analysis indicated that the expressions of hundred genes were significantly altered in simulated microgravity conditions compared to that of normal gravity conditions. Under these conditions genes coding for adaptation to stress are up regulated (sufE and ssrA) and simultaneously genes coding for membrane transporters (ompC, exbB, actP, mgtA, cysW and nikB) and carbohydrate catabolic processes (ldcC, ptsA, rhaD and rhaS) are down regulated. The enhanced growth in simulated gravity conditions may be because of the adequate supply of energy/reducing equivalents and up regulation of genes involved in DNA replication (srmB) and repression of the genes encoding for nucleoside metabolism (dfp, pyrD and spoT). In addition, E. coli cultured in LB medium supplemented with glycerol (so as to protect the cells from freezing temperatures) do not exhibit multiple stress responses that are normally observed when cells are exposed to microgravity in LB medium without glycerol.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=23472115 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589462 PMC3589462]<br />
Online version:[http://dx.doi.org/10.1371/journal.pone.0057860 10.1371/journal.pone.0057860]<br />
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{{LitSignificance}}<br />
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==References==<br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:23472115&diff=1490535PMID:234721152013-10-06T14:30:45Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:20855516&diff=1400736PMID:208555162013-08-10T11:30:48Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''de Pace, F, Nakazato, G, Pacheco, A, de Paiva, JB, Sperandio, V and da Silveira, WD''' (2010) The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain. ''Infect. Immun.'' '''78''':4990-8<br />
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Avian pathogenic Escherichia coli (APEC) strains frequently cause extraintestinal infections and are responsible for significant economic losses in the poultry industry worldwide. APEC isolates are closely related to human extraintestinal pathogenic E. coli (ExPEC) strains and may also act as pathogens for humans. Known APEC virulence factors include adhesins such as type 1 fimbriae and curli, iron acquisition systems, and cytotoxins. Here we show that APEC strain SEPT362, isolated from a septicemic hen, expresses a type VI secretion system (T6SS); causes cytoskeleton rearrangements; and invades epithelial cells, replicates within macrophages, and causes lethal disease in chicks. To assess the contribution of the T6SS to SEPT362 pathogenesis, we generated two mutants, hcp (which encodes a protein suggested to be both secreted and a structural component of the T6SS) and clpV (encoding the T6SS ATPase). Both mutants showed decreased adherence and actin rearrangement on epithelial cells. However, only the hcp mutant presented a mild decrease in its ability to invade epithelial cells, and none of these mutants were defective for intramacrophage replication. Transcriptome studies showed that the level of expression of type 1 fimbriae was decreased in these mutants, which may account for the diminished adhesion and invasion of epithelial cells. The T6SS seems to be important for the disease process, given that both mutants were attenuated for infection in chicks. These results suggest that the T6SS influences the expression of type 1 fimbriae and contributes to APEC pathogenesis.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20855516 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326 PMC2981326]<br />
Online version:[http://dx.doi.org/10.1128/IAI.00531-10 10.1128/IAI.00531-10]<br />
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Animals; Bacterial Adhesion/physiology; Bacterial Secretion Systems/physiology; Chickens/microbiology; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli/pathogenicity; Escherichia coli Infections/microbiology; Escherichia coli Infections/veterinary; Fimbriae, Bacterial/metabolism; Gene Expression Regulation, Bacterial/genetics; HeLa Cells/microbiology; Humans; Mutation; Oligonucleotide Array Sequence Analysis; Poultry Diseases/microbiology; Reverse Transcriptase Polymerase Chain Reaction; Sepsis/microbiology; Sepsis/veterinary<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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<annotationlinks/><br />
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<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:20855516&diff=1400735PMID:208555162013-08-10T11:30:47Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:21398637&diff=1400710PMID:213986372013-08-03T20:14:19Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Maciag, A, Peano, C, Pietrelli, A, Egli, T, De Bellis, G and Landini, P''' (2011) In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements. ''Nucleic Acids Res.'' '''39''':5338-55<br />
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Specific promoter recognition by bacterial RNA polymerase is mediated by σ subunits, which assemble with RNA polymerase core enzyme (E) during transcription initiation. However, σ(70) (the housekeeping σ subunit) and σ(S) (an alternative σ subunit mostly active during slow growth) recognize almost identical promoter sequences, thus raising the question of how promoter selectivity is achieved in the bacterial cell. To identify novel sequence determinants for selective promoter recognition, we performed run-off/microarray (ROMA) experiments with RNA polymerase saturated either with σ(70) (Eσ(70)) or with σ(S) (Eσ(S)) using the whole Escherichia coli genome as DNA template. We found that Eσ(70), in the absence of any additional transcription factor, preferentially transcribes genes associated with fast growth (e.g. ribosomal operons). In contrast, Eσ(S) efficiently transcribes genes involved in stress responses, secondary metabolism as well as RNAs from intergenic regions with yet-unknown function. Promoter sequence comparison suggests that, in addition to different conservation of the -35 sequence and of the UP element, selective promoter recognition by either form of RNA polymerase can be affected by the A/T content in the -10/+1 region. Indeed, site-directed mutagenesis experiments confirmed that an A/T bias in the -10/+1 region could improve promoter recognition by Eσ(S).<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21398637 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248 PMC3141248]<br />
Online version:[http://dx.doi.org/10.1093/nar/gkr129 10.1093/nar/gkr129]<br />
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Base Sequence; Conserved Sequence; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Gene Expression Profiling; Mutation; Oligonucleotide Array Sequence Analysis; Promoter Regions, Genetic; Protein Subunits/metabolism; Regulon; Sigma Factor/metabolism; Transcription, Genetic<br />
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{{LitSignificance}}<br />
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== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
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<annotationlinks/><br />
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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br />
{{LitLinks}}<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:21398637&diff=1400709PMID:213986372013-08-03T20:14:18Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:11399091&diff=1400695PMID:113990912013-07-27T13:20:04Z<p>46.161.41.24: Fill PMID: Page!</p>
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'''Heddle, JG, Lu, T, Zhao, X, Drlica, K and Maxwell, A''' (2001) gyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity. ''J. Mol. Biol.'' '''309''':1219-31<br />
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The B subunit of DNA gyrase (GyrB) consists of a 43 kDa N-terminal domain, containing the site of ATP binding and hydrolysis, and a 47 kDa C-terminal domain that is thought to play a role in interactions with GyrA and DNA. In cells containing a deletion of topA (the gene encoding DNA topoisomerase I) a compensatory mutation is found in gyrB. This mutation (gyrB-225) results in a two amino acid insertion in the N-terminal domain of GyrB. We found that cells containing this mutation are more sensitive than wild-type cells to quinolone drugs with respect to bacteriostatic and lethal action. We have characterised the mutant GyrB protein in vitro and found it to have reduced DNA supercoiling, relaxation, ATPase, and cleavage activities. The mutant enzyme is up to threefold more sensitive to quinolones than wild-type. The mutation also increases the affinity of GyrB for GyrA and DNA, while the affinity of quinolone for the enzyme-DNA complex is unaffected. We propose that the loss in activity is due to misfolding of the GyrB-225 protein, providing an example in which misfolding of one protein, DNA gyrase, suppresses a deficiency of another, topoisomerase I. The increased quinolone sensitivity is proposed to be a consequence of an altered conformation of the protein that renders quinolones better able to disrupt, rather than generate, gyrase-drug-DNA complexes.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11399091 PubMed]<br />
Online version:[http://dx.doi.org/10.1006/jmbi.2001.4733 10.1006/jmbi.2001.4733]<br />
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Adenosine Triphosphatases/antagonists & inhibitors; Adenosine Triphosphatases/chemistry; Adenosine Triphosphatases/genetics; Adenosine Triphosphatases/metabolism; Alleles; Amino Acid Substitution/genetics; Anti-Infective Agents/metabolism; Anti-Infective Agents/pharmacology; Ciprofloxacin/metabolism; Ciprofloxacin/pharmacology; DNA Gyrase; DNA Topoisomerases, Type I/deficiency; DNA Topoisomerases, Type I/genetics; DNA Topoisomerases, Type II/chemistry; DNA Topoisomerases, Type II/genetics; DNA Topoisomerases, Type II/metabolism; DNA, Superhelical/chemistry; DNA, Superhelical/genetics; DNA, Superhelical/metabolism; Drug Tolerance; Escherichia coli/drug effects; Escherichia coli/enzymology; Escherichia coli/genetics; Genetic Complementation Test; Kinetics; Models, Molecular; Nucleic Acid Conformation; Oxolinic Acid/metabolism; Oxolinic Acid/pharmacology; Plasmids/chemistry; Plasmids/genetics; Plasmids/metabolism; Protein Binding/drug effects; Protein Folding; Protein Structure, Tertiary; Suppression, Genetic/genetics; Surface Plasmon Resonance; Thermodynamics; Topoisomerase II Inhibitors<br />
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{{LitSignificance}}<br />
<br />
== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
<br />
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<annotationlinks/><br />
<br />
==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br />
{{LitLinks}}<br />
<br />
==See also==<br />
<br />
==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:11399091&diff=1400694PMID:113990912013-07-27T13:20:03Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:4562989&diff=1400693PMID:45629892013-07-27T03:48:54Z<p>46.161.41.24: Fill PMID: Page!</p>
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{| id="J51f3432656dd2" class=" tableEdit PMID_info_table" <br />
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|-<br />
!align=left |Citation<br />
||<br />
'''Falcoz-Kelly, F, Janin, J, Saari, JC, Véron, M, Truffa-Bachi, P and Cohen, GN''' (1972) Revised structure of aspartokinase I-homoserine dehydrogenase I of Escherichia coli K12. Evidence for four identical subunits. ''Eur. J. Biochem.'' '''28''':507-19<br />
|-<br />
!align=left |Abstract<br />
||<br />
No abstract in PubMed<br />
|-<br />
!align=left |Links<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=4562989 PubMed]<br />
<br />
|-<br />
!align=left |Keywords<br />
||<br />
Alcohol Oxidoreductases/analysis; Amino Acid Sequence; Amino Acids/analysis; Aspartic Acid; Autoanalysis; Autoradiography; Chromatography, Gel; Chromatography, Ion Exchange; Cysteine/analysis; Electrophoresis, Polyacrylamide Gel; Escherichia coli/enzymology; Homoserine; Isoelectric Focusing; Light; Macromolecular Substances; Molecular Weight; Peptides/analysis; Phosphotransferases/analysis; Scattering, Radiation; Sodium Dodecyl Sulfate; Spectrophotometry, Ultraviolet; Structure-Activity Relationship; Tryptophan/analysis<br />
<br />
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|}<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
<br />
== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
<br />
==Annotations {{HelpIcon|Help:Literature}}==<br />
<annotationlinks/><br />
<br />
==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br />
{{LitLinks}}<br />
<br />
==See also==<br />
<br />
==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:4562989&diff=1400692PMID:45629892013-07-27T03:48:54Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22047137&diff=1400561PMID:220471372013-07-11T11:55:14Z<p>46.161.41.24: Fill PMID: Page!</p>
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||<br />
'''Lee, JH, Park, JH, Kim, JA, Neupane, GP, Cho, MH, Lee, CS and Lee, J''' (2011) Low concentrations of honey reduce biofilm formation, quorum sensing, and virulence in Escherichia coli O157:H7. ''Biofouling'' '''27''':1095-104<br />
|-<br />
!align=left |Abstract<br />
||<br />
Bacterial biofilms are associated with persistent infections due to their high resistance to antimicrobial agents. Hence, controlling pathogenic biofilm formation is important in bacteria-related diseases. Honey, at a low concentration of 0.5% (v/v), significantly reduced biofilm formation in enterohemorrhagic Escherichia coli O157:H7 without inhibiting the growth of planktonic cells. Conversely, this concentration did not inhibit commensal E. coli K-12 biofilm formation. Transcriptome analyses showed that honey significantly repressed curli genes (csgBAC), quorum sensing genes (AI-2 importer and indole biosynthesis), and virulence genes (LEE genes). Glucose and fructose in the honeys were found to be key components in reducing biofilm formation by E. coli O157:H7 through the suppression of curli production and AI-2 import. Furthermore, honey, glucose and fructose decreased the colonization of E. coli O157:H7 cells on human HT-29 epithelial cells. These results suggest that low concentrations of honey, such as in honeyed water, can be a practical means for reducing the colonization and virulence of pathogenic E. coli O157:H7.<br />
|-<br />
!align=left |Links<br />
||<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22047137 PubMed]<br />
Online version:[http://dx.doi.org/10.1080/08927014.2011.633704 10.1080/08927014.2011.633704]<br />
|-<br />
!align=left |Keywords<br />
||<br />
Bacterial Proteins/metabolism; Biofilms; Escherichia coli K12/physiology; Escherichia coli O157/pathogenicity; Escherichia coli O157/physiology; Fructose; Gene Expression Regulation, Bacterial; Glucose; HT29 Cells; Honey; Humans; Quorum Sensing; Virulence<br />
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<br />
==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
<br />
== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
<br />
==Annotations {{HelpIcon|Help:Literature}}==<br />
<annotationlinks/><br />
<br />
==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br />
{{LitLinks}}<br />
<br />
==See also==<br />
<br />
==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22047137&diff=1400560PMID:220471372013-07-11T11:55:13Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22274708&diff=1400528PMID:222747082013-06-29T22:39:53Z<p>46.161.41.24: Fill PMID: Page!</p>
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||<br />
'''Lee, JH, Kim, YG, Kim, CJ, Lee, JC, Cho, MH and Lee, J''' (2012) Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation. ''Appl. Microbiol. Biotechnol.'' '''96''':1071-8<br />
|-<br />
!align=left |Abstract<br />
||<br />
Pathogenic biofilms have been associated with persistent infections due to their high resistance to antimicrobial agents. To identify nontoxic biofilm inhibitors for enterohemorrhagic Escherichia coli O157:H7, the spent media of a 4,104 Actinomycetes library was screened. The culture spent medium (1%, v/v) of plant pathogen Rhodococcus sp. BFI 332 markedly inhibited E. coli O157:H7 biofilm formation without affecting the growth of planktonic E. coli O157:H7 cells. Rhodococcus sp. BFI 332 produced significant amounts of indole-3-acetaldehyde and indole-3-acetic acid, and the former of which reduced E. coli O157:H7 biofilm formation. Global transcriptome analyses showed that indole-3-acetaldehyde most repressed two curli operons, csgBAC and csgDEFG, and induced tryptophanase (tnaAB) in E. coli O157:H7 biofilm cells. Electron microscopy showed that spent medium of Rhodococcus sp. BFI 332 and indole-3-acetaldehyde reduced curli production in E. coli O157:H7. The spent medium of Rhodococcus sp. BFI 332 also significantly reduced the biofilm formation of Staphylococcus aureus and Staphylococcus epidermidis. Overall, this study suggests that indole derivatives are present in the Actinomycetes strains and they can be used as biofilm inhibitors against pathogenic bacteria.<br />
|-<br />
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||<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22274708 PubMed]<br />
Online version:[http://dx.doi.org/10.1007/s00253-012-3881-y 10.1007/s00253-012-3881-y]<br />
|-<br />
!align=left |Keywords<br />
||<br />
Biofilms/drug effects; Escherichia coli O157/drug effects; Escherichia coli O157/genetics; Escherichia coli O157/growth & development; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Gene Expression Regulation, Bacterial/drug effects; Indoles/metabolism; Indoles/pharmacology; Rhodococcus/genetics; Rhodococcus/metabolism; Staphylococcus aureus/drug effects; Staphylococcus aureus/physiology<br />
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<br />
==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
<br />
== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
<br />
==Annotations {{HelpIcon|Help:Literature}}==<br />
<annotationlinks/><br />
<br />
==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br />
{{LitLinks}}<br />
<br />
==See also==<br />
<br />
==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22274708&diff=1400527PMID:222747082013-06-29T22:39:53Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22505047&diff=1400526PMID:225050472013-06-29T22:22:00Z<p>46.161.41.24: Fill PMID: Page!</p>
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|-<br />
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||<br />
'''Gupta, P, Swanberg, JC and Lee, KH''' A single nucleotide polymorphism in ycdC alters tRNA synthetase expression and results in hypersecretion in Escherichia coli. ''Biotechnol. Prog.'' '''28''':646-53<br />
|-<br />
!align=left |Abstract<br />
||<br />
The most important approach to the development of platform organisms for recombinant protein production relies on random mutagenesis and phenotypic selection. Complex phenotypes, including those associated with significantly elevated expression and secretion of heterologous proteins, are the result of multiple genomic mutations. Using next generation sequencing, a parent and derivative hypersecreter strain (B41) of Escherichia coli were sequenced with an average coverage of 52.8X and 55X, respectively. A new base-pair calling program, revealed a single nucleotide polymorphism in the B41 genome at position 1,074,787, resulting in translation termination near the N-terminus of a transcriptional regulator protein, RutR, coded by the ycdC gene. We verified the hypersecretion phenotype in a ycdC::Tn5 mutant and observed a 3.4-fold increase in active hemolysin secretion, consistent with the increase observed in B41 strain. mRNA expression profiling showed decreased expression of tRNA-synthetases and some amino acid transporters in the ycdC::Tn5 mutant. This study demonstrates the power of next generation sequencing to characterize mutants leading to successful metabolic engineering strategies for strain improvement.<br />
|-<br />
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||<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22505047 PubMed]<br />
Online version:[http://dx.doi.org/10.1002/btpr.1550 10.1002/btpr.1550]<br />
|-<br />
!align=left |Keywords<br />
||<br />
Amino Acyl-tRNA Synthetases/genetics; Base Sequence; Blotting, Western; DNA Primers; DNA, Bacterial/genetics; Escherichia coli/genetics; Genes, Bacterial; Molecular Sequence Data; Polymorphism, Single Nucleotide; RNA, Messenger/genetics; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; Sequence Homology, Nucleic Acid<br />
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<br />
==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
<br />
== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
<br />
==Annotations {{HelpIcon|Help:Literature}}==<br />
<annotationlinks/><br />
<br />
==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br />
{{LitLinks}}<br />
<br />
==See also==<br />
<br />
==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22505047&diff=1400525PMID:225050472013-06-29T22:21:59Z<p>46.161.41.24: New PMID: Page!</p>
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<div></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22645336&diff=1400516PMID:226453362013-06-28T12:40:05Z<p>46.161.41.24: Fill PMID: Page!</p>
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||<br />
'''Le Gac, M, Plucain, J, Hindré, T, Lenski, RE and Schneider, D''' (2012) Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli. ''Proc. Natl. Acad. Sci. U.S.A.'' '''109''':9487-92<br />
|-<br />
!align=left |Abstract<br />
||<br />
Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.<br />
|-<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22645336 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386082 PMC3386082]<br />
Online version:[http://dx.doi.org/10.1073/pnas.1207091109 10.1073/pnas.1207091109]<br />
|-<br />
!align=left |Keywords<br />
||<br />
Cluster Analysis; Ecology; Escherichia coli/genetics; Escherichia coli/growth & development; Evolution, Molecular; Gene Expression Profiling<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
<br />
== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
<br />
==Annotations {{HelpIcon|Help:Literature}}==<br />
<annotationlinks/><br />
<br />
==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br />
{{LitLinks}}<br />
<br />
==See also==<br />
<br />
==References==<br />
{{RefHelp}}<br />
<references/></div>46.161.41.24https://ecoliwiki.org/colipedia/index.php?title=PMID:22645336&diff=1400515PMID:226453362013-06-28T12:40:05Z<p>46.161.41.24: New PMID: Page!</p>
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