EcoliWiki - User contributions [en]

https://ecoliwiki.org/colipedia/api.php?action=feedcontributions&feedformat=atom&user=165.91.51.61 EcoliWiki - User contributions [en] 2026-11-04T15:20:43Z User contributions MediaWiki 1.43.11 https://ecoliwiki.org/colipedia/index.php?title=PMID:19767571&diff=1374419 PMID:19767571 2013-02-01T23:33:21Z

<p>165.91.51.61: Fill PMID: Page!</p> <hr /> <div>{{RightTOC}}<br /> <br /> <br /> {| id="Z510c50c0bf411" class=" tableEdit PMID_info_table" <br /> <br /> |-<br /> !align=left |Citation<br /> ||<br /> '''Masuda, T , Saito, N , Tomita, M and Ishihama, Y ''' (2009) Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. ''Mol. Cell Proteomics'' '''8''':2770-7<br /> |-<br /> !align=left |Abstract<br /> ||<br /> We developed a sample preparation protocol for rapid and unbiased analysis of the membrane proteome using an alimentary canal-mimicking system in which proteases are activated in the presence of bile salts. In this rapid and unbiased protocol, immobilized trypsin is used in the presence of deoxycholate and lauroylsarcosine to increase digestion efficiency as well as to increase the solubility of the membrane proteins. Using 22.5 microg of Escherichia coli whole cell lysate, we quantitatively demonstrated that membrane proteins were extracted and digested at the same level as soluble proteins without any solubility-related bias. The recovery of membrane proteins was independent of the number of transmembrane domains per protein. In the analysis of the membrane-enriched fraction from 22.5 microg of E. coli cell lysate, the abundance distribution of the membrane proteins was in agreement with that of the membrane protein-coding genes when this protocol, coupled with strong cation exchange prefractionation prior to nano-LC-MS/MS analysis, was used. Because this protocol allows unbiased sample preparation, protein abundance estimation based on the number of observed peptides per protein was applied to both soluble and membrane proteins simultaneously, and the copy numbers per cell for 1,453 E. coli proteins, including 545 membrane proteins, were successfully obtained. Finally, this protocol was applied to quantitative analysis of guanosine tetra- and pentaphosphate-dependent signaling in E. coli wild-type and relA knock-out strains.<br /> |-<br /> !align=left |Links<br /> ||<br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19767571 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2816013 PMC2816013]<br /> Online version:[http://dx.doi.org/10.1074/mcp.M900240-MCP200 10.1074/mcp.M900240-MCP200]<br /> |-<br /> !align=left |Keywords<br /> ||<br /> Chemotaxis; Databases, Protein; Escherichia coli/cytology; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli Proteins/analysis; Flagella/metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Membrane Proteins/analysis; Membrane Proteins/chemistry; Protein Structure, Tertiary; Protein Subunits/metabolism; Proteome/analysis; Proteomics/methods; RNA, Messenger/genetics; RNA, Messenger/metabolism; Solubility; Surface-Active Agents/metabolism<br /> <br /> |- class="tableEdit_footer" <br /> |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182902.Z510c50c0bf411&page=182902&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table]</span> ||<br /> |}<br /> <br /> <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 /> <protect><br /> <br /> {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="M510c50c13209b" class=" tableEdit GO_table_reference dataTable" <br /> |- {{table heading style}}<br /> !|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> <br /> |- class="tableEdit_footer" <br /> |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182902.M510c50c13209b&page=182902&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table]</span> || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==See also==<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:19767571&diff=1374418 PMID:19767571 2013-02-01T23:33:20Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:16996538&diff=1359526 PMID:16996538 2011-09-29T21:38:24Z

<p>165.91.51.61: Fill PMID: Page!</p> <hr /> <div>{{RightTOC}}<br /> <protect><br /> <span style = 'font-size: large'> '''Baxter, K, Lee, J, Minakhin, L, Severinov, K and Hinton, DM''' (2006) Mutational analysis of sigma70 region 4 needed for appropriation by the bacteriophage T4 transcription factors AsiA and MotA.''J. Mol. Biol.'' '''363''':931-44</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || <protect>Transcriptional activation of bacteriophage T4 middle promoters requires sigma70-containing Escherichia coli RNA polymerase, the T4 activator MotA, and the T4 co-activator AsiA. T4 middle promoters contain the sigma70 -10 DNA element. However, these promoters lack the sigma70 -35 element, having instead a MotA box centered at -30, which is bound by MotA. Previous work has indicated that AsiA and MotA interact with region 4 of sigma70, the C-terminal portion that normally contacts -35 DNA and the beta-flap structure in core. AsiA binding prevents the sigma70/beta-flap and sigma70/-35 DNA interactions, inhibiting transcription from promoters that require a -35 element. To test the importance of residues within sigma70 region 4 for MotA and AsiA function, we investigated how sigma70 region 4 mutants interact with AsiA, MotA, and the beta-flap and function in transcription assays in vitro. We find that alanine substitutions at residues 584-588 (region 4.2) do not impair the interaction of region 4 with the beta-flap or MotA, but they eliminate the interaction with AsiA and prevent AsiA inhibition and MotA/AsiA activation. In contrast, alanine substitutions at 551-552, 554-555 (region 4.1) eliminate the region 4/beta-flap interaction, significantly impair the AsiA/sigma70 interaction, and eliminate AsiA inhibition. However, the 4.1 mutant sigma70 is still fully competent for activation if both MotA and AsiA are present. A previous NMR structure shows AsiA binding to sigma70 region 4, dramatically distorting regions 4.1 and 4.2 and indirectly changing the conformation of the MotA interaction site at the sigma70 C terminus. Our analyses provide biochemical relevance for the sigma70 residues identified in the structure, indicate that the interaction of AsiA with sigma70 region 4.2 is crucial for activation, and support the idea that AsiA binding facilitates an interaction between MotA and the far C terminus of sigma70.</protect><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' ||<br /> * [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16996538 PubMed]<br /> Online version:[http://dx.doi.org/10.1016/j.jmb.2006.08.074 10.1016/j.jmb.2006.08.074]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {| id="Z4e84e550a3739" class=" tableEdit GO_table_reference dataTable" <br /> |- {{table heading style}}<br /> !|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> <br /> |- class="tableEdit_footer" <br /> |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.180697.Z4e84e550a3739&page=180697&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table]</span> || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==See also==<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:16996538&diff=1359525 PMID:16996538 2011-09-29T21:38:24Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:18677321&diff=1200088 PMID:18677321 2010-10-05T18:20:30Z

<p>165.91.51.61: Fill PMID: Page!</p> <hr /> <div>{{RightTOC}}<br /> <protect><br /> <span style = 'font-size: large'> '''Butland, G, Babu, M, Díaz-Mejía, JJ, Bohdana, F, Phanse, S, Gold, B, Yang, W, Li, J, Gagarinova, AG, Pogoutse, O, Mori, H, Wanner, BL, Lo, H, Wasniewski, J, Christopolous, C, Ali, M, Venn, P, Safavi-Naini, A, Sourour, N, Caron, S, Choi, JY, Laigle, L, Nazarians-Armavil, A, Deshpande, A, Joe, S, Datsenko, KA, Yamamoto, N, Andrews, BJ, Boone, C, Ding, H, Sheikh, B, Moreno-Hagelseib, G, Greenblatt, JF and Emili, A''' (2008) eSGA: E. coli synthetic genetic array analysis.''Nat. Methods'' '''5''':789-95</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || <protect>Physical and functional interactions define the molecular organization of the cell. Genetic interactions, or epistasis, tend to occur between gene products involved in parallel pathways or interlinked biological processes. High-throughput experimental systems to examine genetic interactions on a genome-wide scale have been devised for Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster, but have not been reported previously for prokaryotes. Here we describe the development of a quantitative screening procedure for monitoring bacterial genetic interactions based on conjugation of Escherichia coli deletion or hypomorphic strains to create double mutants on a genome-wide scale. The patterns of synthetic sickness and synthetic lethality (aggravating genetic interactions) we observed for certain double mutant combinations provided information about functional relationships and redundancy between pathways and enabled us to group bacterial gene products into functional modules.</protect><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' ||<br /> * [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18677321 PubMed]<br /> Online version:[http://dx.doi.org/10.1038/nmeth.1239 10.1038/nmeth.1239]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {| id="M4cab6c6dcbb8b" class=" tableEdit GO_table_reference" <br /> |- {{table heading style}}<br /> !|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> <br /> |- class="tableEdit_footer" <br /> |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.176222.M4cab6c6dcbb8b&page=176222&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table]</span> || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==See also==<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:18677321&diff=1200087 PMID:18677321 2010-10-05T18:20:29Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:11715047&diff=1080787 PMID:11715047 2010-04-27T19:11:09Z

<p>165.91.51.61: Fill PMID: Page!</p> <hr /> <div>{{RightTOC}}<br /> <protect><br /> <span style = 'font-size: large'> '''Peters, JE and Craig, NL''' (2001) Tn7: smarter than we thought.''Nat. Rev. Mol. Cell Biol.'' '''2''':806-14</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || <protect>A notable feature of transposable elements--segments of DNA that can move from one position to another in genomes--is that they are highly prevalent, despite the fact that their translocation can result in mutation. The bacterial transposon Tn7 uses an elaborate system of target-site selection pathways that favours the dispersal of Tn7 in diverse hosts as well as minimizing its negative effects.</protect><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' ||<br /> * [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11715047 PubMed]<br /> Online version:[http://dx.doi.org/10.1038/35099006 10.1038/35099006]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {| id="M4bd736cdb7c8b" class=" tableEdit GO_table_reference" <br /> |- {{table heading style}}<br /> !|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> <br /> |- class="tableEdit_footer" <br /> |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171923.M4bd736cdb7c8b&page=171923&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table]</span> || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==See also==<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:11715047&diff=1080786 PMID:11715047 2010-04-27T19:11:09Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:12093750&diff=1080785 PMID:12093750 2010-04-27T19:10:07Z

<p>165.91.51.61: Fill PMID: Page!</p> <hr /> <div>{{RightTOC}}<br /> <protect><br /> <span style = 'font-size: large'> '''Skelding, Z, Sarnovsky, R and Craig, NL''' (2002) Formation of a nucleoprotein complex containing Tn7 and its target DNA regulates transposition initiation.''EMBO J.'' '''21''':3494-504</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || <protect>Tn7 insertion into its specific target site, attTn7, is mediated by the proteins TnsA, TnsB, TnsC and TnsD. The double-strand breaks that separate Tn7 from the donor DNA require the Tns proteins, the transposon and an attTn7 target DNA, suggesting that a prerequisite for transposition is the formation of a nucleoprotein complex containing TnsABC+D, and these DNAs. Here, we identify a TnsABC+D transposon-attTn7 complex, and demonstrate that it is a transposition intermediate. We demonstrate that an interaction between TnsB, the transposase subunit that binds to the transposon ends, and TnsC, the target DNA-binding protein that controls the activity of the transposase, is essential for assembly of the TnsABC+D transposon-attTn7 complex. We also show that certain TnsB residues are required for recombination because they mediate a TnsB-TnsC interaction critical to formation of the TnsABC+D transposon-attTn7 complex. We demonstrate that TnsA, the other transposase subunit, which also interacts with TnsC, greatly stabilizes the TnsABC+D transposon-attTn7 complex. Thus multiple interactions between the transposase subunits, TnsA and TnsB, and the target-binding transposase activator, TnsC, control Tn7 transposition.</protect><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' ||<br /> * [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12093750 PubMed]<br /> Online version:[http://dx.doi.org/10.1093/emboj/cdf347 10.1093/emboj/cdf347]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {| id="L4bd7368f55868" class=" tableEdit GO_table_reference" <br /> |- {{table heading style}}<br /> !|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> <br /> |- class="tableEdit_footer" <br /> |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171922.L4bd7368f55868&page=171922&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table]</span> || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==See also==<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:12093750&diff=1080784 PMID:12093750 2010-04-27T19:10:07Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:12618467&diff=1080783 PMID:12618467 2010-04-27T19:09:28Z

<p>165.91.51.61: Fill PMID: Page!</p> <hr /> <div>{{RightTOC}}<br /> <protect><br /> <span style = 'font-size: large'> '''Peters, JE, Thate, TE and Craig, NL''' (2003) Definition of the Escherichia coli MC4100 genome by use of a DNA array.''J. Bacteriol.'' '''185''':2017-21</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || <protect>We have used an Escherichia coli K-12 whole-genome array based on the DNA sequence of strain MG1655 as a tool to identify deletions in another E. coli K-12 strain, MC4100, by probing the array with labeled chromosomal DNA. Despite the continued widespread use of MC4100 as an experimental system, the specific genetic relationship of this strain to the sequenced K-12 derivative MG1655 has not been resolved. MC4100 was found to contain four deletions, ranging from 1 to 97 kb in size. The exact nature of three of the deletions was previously unresolved, and the fourth deletion was altogether unknown.</protect><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' ||<br /> * [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12618467 PubMed]<br /> <br /> |}<br /> </protect><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 /> <protect><br /> <br /> {| id="Y4bd73668bdafc" class=" tableEdit GO_table_reference" <br /> |- {{table heading style}}<br /> !|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> <br /> |- class="tableEdit_footer" <br /> |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171921.Y4bd73668bdafc&page=171921&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table]</span> || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==See also==<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:12618467&diff=1080782 PMID:12618467 2010-04-27T19:09:28Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:14592987&diff=1080781 PMID:14592987 2010-04-27T19:09:01Z

<p>165.91.51.61: Fill PMID: Page!</p> <hr /> <div>{{RightTOC}}<br /> <protect><br /> <span style = 'font-size: large'> '''Skelding, Z, Queen-Baker, J and Craig, NL''' (2003) Alternative interactions between the Tn7 transposase and the Tn7 target DNA binding protein regulate target immunity and transposition.''EMBO J.'' '''22''':5904-17</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || <protect>The Tn7 transposon avoids inserting into a target DNA that contains a pre-existing copy of Tn7. This phenomenon, known as 'target immunity', is established when TnsB, a Tn7 transposase subunit, binds to Tn7 sequences in the target DNA and mediates displacement of TnsC, a critical transposase activator, from the DNA. Paradoxically, TnsB-TnsC interactions are also required to promote transposon insertion. We have probed Tn7 target immunity by isolating TnsB mutants that mediate more frequent insertions into a potentially immune target DNA because they fail to provoke dissociation of TnsC from the DNA. We show that a single region of TnsB mediates the TnsB-TnsC interaction that underlies both target immunity and transposition, but that TnsA, the other transposase subunit, channels the TnsB-TnsC interaction toward transposition.</protect><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' ||<br /> * [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14592987 PubMed]<br /> Online version:[http://dx.doi.org/10.1093/emboj/cdg551 10.1093/emboj/cdg551]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {| id="T4bd7364cdb128" class=" tableEdit GO_table_reference" <br /> |- {{table heading style}}<br /> !|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> <br /> |- class="tableEdit_footer" <br /> |<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171920.T4bd7364cdb128&page=171920&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table]</span> || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==See also==<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:14592987&diff=1080780 PMID:14592987 2010-04-27T19:09:00Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:2113913&diff=357231 PMID:2113913 2008-02-08T00:55:51Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Brusca, JS, Chastain, CJ and Golden, JW''' (1990) Expression of the Anabaena sp. strain PCC 7120 xisA gene from a heterologous promoter results in excision of the nifD element.''J. Bacteriol.'' '''172''':3925-31</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || An 11-kilobase-pair element interrupts the nifD gene in vegetative cells of Anabaena sp. strain PCC 7120. The nifD element normally excises only from the chromosomes of cells that differentiate into nitrogen-fixing heterocysts. The xisA gene contained within the element is required for the excision. Shuttle vectors containing the Escherichia coli tac consensus promoter fused to various 5' deletions of the xisA gene were constructed and conjugated into Anabaena sp. strain PCC 7120 cells. Some of the expression plasmids resulted in excision of the nifD element in a high proportion of vegetative cells. Excision of the element required deletion of an xisA 5' regulatory region which presumably blocks expression in Anabaena sp. strain PCC 7120 vegetative cells but not in E. coli. Strains lacking the nifD element grew normally in medium containing a source of combined nitrogen and showed normal growth and heterocyst development in medium lacking combined nitrogen. The xisA gene was shown to be the only Anabaena gene required for the proper rearrangement in E. coli of a plasmid containing the borders of the nifD element.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2113913 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241485' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.P47aba896f0436&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:2197600&diff=357230 PMID:2197600 2008-02-08T00:55:45Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Gilson, E, Perrin, D and Hofnung, M''' (1990) DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization.''Nucleic Acids Res.'' '''18''':3941-52</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to the DNA polymerase I (Pol I). This constitutes the first indication for a specific interaction between Pol I and a duplex DNA. This interaction requires the presence of PU. It was confirmed and analyzed by native gel electrophoresis and DNase I footprinting experiments. The other activity contained at least five polypeptides. Its binding to PU DNA sequences was confirmed by native gel electrophoresis. Implications for the possible origin and functions of PU are discussed.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2197600 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241484' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Q47aba8913ecaf&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:2092362&diff=357229 PMID:2092362 2008-02-08T00:55:39Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Gilson, E, Bachellier, S, Perrin, S, Perrin, D, Grimont, PA, Grimont, F and Hofnung, M''' Palindromic unit highly repetitive DNA sequences exhibit species specificity within Enterobacteriaceae.''Res. Microbiol.'' '''141''':1103-16</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Palindromic units (PU, or REP for repetitive extragenic palindrome) constitute a family of DNA sequences of 40 nucleotides which is highly repeated in the genome of Escherichia coli. We analysed the presence of PU sequences in 99 different bacterial genomes by cross-hybridization. When PU sequences were used as a probe, only DNA from Enterobacteriaceae closely related to E. coli exhibited an appreciable hybridization signal: Shigella sonnei, Shigella boydii, Salmonella enteritica serotype Typhimurium, Citrobacter freundii and Levinea malonatica. Furthermore, these bacteria could be divided into two groups which corresponded to a slight difference in their PU sequence: the E. coli group includes S. sonnei and S. boydii; the S. enteritica serotype Typhimurium group includes C. freundii and L. malonatica.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2092362 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241483' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.M47aba88b82060&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1833192&diff=357228 PMID:1833192 2008-02-08T00:55:33Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Mottl, H and Keck, W''' (1991) Purification of penicillin-binding protein 4 of Escherichia coli as a soluble protein by dye-affinity chromatography.''Eur. J. Biochem.'' '''200''':767-73</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The dacB gene of Escherichia coli, coding for penicillin-binding protein 4 (PBP4) was cloned under the control of the phage lambda pR promoter and cro gene translation signals. Depression of the phage lambda promoter for 2 h at 42 degrees C in E. coli led to the maximum over-production of PBP4 to 3.8% of the total soluble protein. Expression at 42 degrees C but not at 40 degrees C or 37 degrees C led to incomplete processing and aggregation of the preform of PBP4. Cibacron navyblue 2G-E was selected from a collection of triazine dyes as having a high affinity for PBP4. The immobilised dye was used in a two-step procedure to isolated 374 mg PBP4 from the soluble fraction of 125 g (wet mass) cells of the over-producing strain, with a recovery of 63.2% and a final purity of 99% as determined by active-site titration with radiolabelled penicillin. Saturation of PBP4 with various beta-lactam derivatives did not abolish binding to the dye material, nor was PBP4 eluted by addition of beta-lactams from the dye matrix. PBP4 behaved as a soluble protein throughout the purification, that was performed in the complete absence of detergents. Furthermore, in flotation experiments on sucrose density gradients and in Triton X-114 fractionation experiments, it showed the characteristics of a soluble protein. Cibacron navyblue 2G-E showed class specificity for all E. coli PBP except PBP3 and could be used for the isolation of these PBP from membrane extracts.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1833192 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241482' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.E47aba885c6fb5&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1846849&diff=357227 PMID:1846849 2008-02-08T00:55:28Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Lloyd, RG and Buckman, C''' (1991) Genetic analysis of the recG locus of Escherichia coli K-12 and of its role in recombination and DNA repair.''J. Bacteriol.'' '''173''':1004-11</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || We describe a transposon insertion that reduces the efficiency of homologous recombination and DNA repair in Escherichia coli. The insertion, rec-258, was located between pyrE and dgo at min 82.1 on the current linkage map. On the basis of linkage to pyrE and complementation studies with the cloned rec+ gene, rec-258 was identified as an allele of the recG locus first reported by Storm et al. (P. K. Storm, W. P. M. Hoekstra, P. G. De Haan, and C. Verhoef, Mutat. Res. 13:9-17, 1971). The recG258 mutation confers sensitivity to mitomycin C and UV light and a 3- to 10-fold deficiency in conjugational recombination in wild-type, recB recC sbcA, and recB recC sbcB sbcC genetic backgrounds. It does not appear to affect plasmid recombination in the wild-type. A recG258 single mutant is also sensitive to ionizing radiation. The SOS response is induced normally, although the basal level of expression is elevated two- to threefold. Further genetic studies revealed that recB recG and recG recJ double mutants are much more sensitive to UV light than the respective single mutants in each case. However, no synergistic interactions were discovered between recG258 and mutations in recF, recN, or recQ. It is concluded that recG does not fall within any of the accepted groups of genes that affect recombination and DNA repair.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1846849 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241481' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.A47aba88018af6&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:2071041&diff=357226 PMID:2071041 2008-02-08T00:55:22Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Touati, D''' (1991) The molecular genetics of superoxide dismutase in E. coli.''Free Radic. Res. Commun.'' '''12-13 Pt 1''':379-82</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The biological role and the regulation of superoxide dismutase (SOD) in E. coli have been investigated using genetics. Cloning of both E. coli SOD genes permitted construction of mutants completely lacking SOD. The conditional oxygen sensitivity of those mutants, together with their increased mutation rate, demonstrated the essential biological role of SOD. SOD-deficient mutants constitute a powerful tool to assess a possible role of O-2 or SOD in biological processes. Complementation of their deficiencies by the expression of SOD originating from a different organism is used for screening libraries for SOD genes of other species. Regulation of MnSOD has been studied using protein and operon fusions with the lactose operon, and isolating regulation mutants. These studies reveal multiregulation of MnSOD including response to the superoxide mediated oxidative stress and response to variations of the intracellular redox state induced by metabolic changes.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2071041 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241480' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Y47aba87a61d48&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1829835&diff=357225 PMID:1829835 2008-02-08T00:55:16Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Connolly, B, Parsons, CA, Benson, FE, Dunderdale, HJ, Sharples, GJ, Lloyd, RG and West, SC''' (1991) Resolution of Holliday junctions in vitro requires the Escherichia coli ruvC gene product.''Proc. Natl. Acad. Sci. U.S.A.'' '''88''':6063-7</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || In previous studies, Holliday junctions generated during RecA-mediated strand-exchange reactions were resolved by fractionated Escherichia coli extracts. We now report the specific binding and cleavage of synthetic Holliday junctions (50 base pairs long) by a fraction purified by chromatography on DEAE-cellulose, phosphocellulose, and single-stranded DNA-cellulose. The cleavage reaction provided a sensitive assay with which to screen extracts prepared from recombination/repair-deficient mutants. Cells with mutations in ruvC lack the nuclease activity that cleaves synthetic Holliday junctions in vitro. This deficiency was restored by a multicopy plasmid carrying a ruvC+ gene that overexpressed junction-resolving activity. The UV sensitivity and deficiency in recombinational repair of DNA exhibited by ruv mutants lead us to suggest that RuvC resolves Holliday junctions in vivo.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1829835 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241479' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.H47aba874a8f31&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1885508&diff=357224 PMID:1885508 2008-02-08T00:55:11Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Dimri, GP, Ames, GF, D'Ari, L and Rabinowitz, JC''' (1991) Physical map location of the Escherichia coli gene encoding the bifunctional enzyme 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methenyl-tetrahydrofolate cyclohydrolase.''J. Bacteriol.'' '''173''':5251</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1885508 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241478' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.V47aba86eed1ee&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1748668&diff=357223 PMID:1748668 2008-02-08T00:55:05Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''D'Ari, L and Rabinowitz, JC''' (1991) Purification, characterization, cloning, and amino acid sequence of the bifunctional enzyme 5,10-methylenetetrahydrofolate dehydrogenase/5,10-methenyltetrahydrofolate cyclohydrolase from Escherichia coli.''J. Biol. Chem.'' '''266''':23953-8</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || We have purified the enzyme 5,10-methylenetetrahydrofolate dehydrogenase (EC 1.5.1.5) from Escherichia coli to homogeneity by a newly devised procedure. The enzyme has been purified at least 2,000-fold in a 31% yield. The specific activity of the enzyme obtained is 7.4 times greater than any previous preparation from this source. The purified enzyme is specific for NADP. The protein also contains 5,10-methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9) activity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and behavior on a molecular sieving column suggest that the enzyme is a dimer of identical subunits. We have cloned the E. coli gene coding for the enzyme through the use of polymerase chain reaction based on primers designed from the NH2 terminal analysis of the isolated enzyme. We sequenced the gene. The derived amino acid sequence of the enzyme contains 287 amino acids of Mr 31,000. The sequence shows 50% identity to two bifunctional mitochondrial enzymes specific for NAD, and 40-45% identity to the presumed dehydrogenase/cyclohydrolase domains of the trifunctional C1-tetrahydrofolate synthase of yeast mitochondria and cytoplasm and human and rat cytoplasm. An identical sequence of 14 amino acids with no gaps is present in all 7 sequences.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1748668 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241477' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.O47aba86938ddd&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1989972&diff=357222 PMID:1989972 2008-02-08T00:54:59Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Williams, JS and Rosevear, PR''' (1991) Nuclear Overhauser effect studies on the conformations of Mg(alpha,beta-methylene)ATP bound to Escherichia coli methionyl-tRNA synthetase.''J. Biol. Chem.'' '''266''':2089-98</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Internuclear distances obtained from nuclear Overhauser effects were used in combination with a distance geometry algorithm to determine the conformation of Mg(alpha,beta-methylene)ATP bound to the Escherichia coli truncated methionyl-tRNA synthetase (delta MTS) both in the absence and presence of cognate and noncognate amino acids. Mg(alpha,beta-methylene)ATP, a nonhydrolyzable analog of ATP, was used to prevent hydrolysis of the nucleotide in the presence of either cognate or noncognate amino acids. Kinetic analysis showed that Mg(alpha,beta-methylene)ATP was a linear competitive inhibitor with respect to ATP in the ATP-pyrophosphate exchange reaction with a Ki = 1.2 mM. The pattern of internuclear Overhauser effects on Mg(alpha,beta-methylene)ATP bound to delta MTS was qualitatively consistent only with an anti glycosidic torsional angle, suggesting that the adenosine portion of the nucleotide is uniquely oriented in the binary enzyme-nucleotide complex. Nearly identical patterns of nuclear Overhauser effects were also observed in ternary complexes containing either cognate L-methionine or noncognate L-homocysteine amino acids. Distance geometry calculations permitted the range and conformational space of the allowed adenine-ribose glycosidic torsional angles in each of the complexes to be better defined and compared. Average adenine-ribose glycosidic torsional angles for enzyme-bound Mg(alpha,beta-methylene)ATP of -106 +/- 9 degrees, -99 +/- 11 degrees, and -97 +/- 11 degrees were determined for the delta MTS.Mg(alpha,beta-methylene)ATP, delta MTS.Mg(alpha,beta-methylene)ATP.L-methionine, and delta MTS.Mg(alpha,beta-methylene)ATP.L-homocysteine complexes, respectively. Comparison of the three enzyme-bound conformations showed that a single nucleotide structure having an adenine-ribose glycosidic torsional angle of -98 degrees with a 3'-endo to O4'-exo ribose sugar pucker was, within error, consistent with the experimental internuclear distances obtained in all three complexes. The nearly identical anti glycosidic torsional angles observed in all three complexes demonstrates that the conformation of the adenosine moiety of the enzyme-bound nucleotide is not sensitive to the presence or the nature of the amino acid bound at the aminoacyladenylate site. Therefore, conformational changes known to occur in the methionyl-tRNA synthetase upon ligand binding appear not to alter the bound conformation of the nucleotide. Information on the conformation and arrangement of substrates bound at the aminoacyladenylate site of delta MTS is necessary for understanding the molecular mechanisms involved in amino acid activation and discrimination.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1989972 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241476' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47aba8637a68a&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:2025282&diff=357221 PMID:2025282 2008-02-08T00:54:53Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Williams, JS and Rosevear, PR''' (1991) Nuclear overhauser effect studies of the conformations of Mg(alpha, beta-methylene)ATP bound to E. coli isoleucyl-tRNA synthetase.''Biochem. Biophys. Res. Commun.'' '''176''':682-9</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Internuclear distances obtained from transferred nuclear Overhauser effects were used in combination with distance geometry calculations to define the E. coli isoleucyl-tRNA synthetase bound conformation of Mg(alpha, beta-methylene)ATP both in the absence and in the presence of the cognate and noncognate amino acids L-isoleucine and L-valine, respectively. A single nucleotide structure having an anti adenine-ribose glycosidic torsional angle of -114 degrees was found to satisfy the experimental distance constraints. The nearly identical anti glycosidic torsional angles observed in all three complexes demonstrate that the conformation of the adenosine moiety of the enzyme-bound nucleotide is not sensitive to the presence or to the nature of the amino acid bound at the aminoacyladenylate site. In addition, the acceptable range of Mg(alpha, beta-methylene)ATP conformations bound to the E. coli isoleucyl-tRNA synthetase was found to be nearly identical to that previously determined for the E. coli methionyl-tRNA synthetase (Williams and Rosevear (1991) J. Biol. Chem. 266, 2089-2098). Thus, the predicted structural homology between the isoleucyl- and methionyl-tRNA synthetases, both members of the same class of synthetases on the basis of common consensus sequences, is further supported by consensus enzyme-bound nucleotide conformations.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2025282 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241475' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.H47aba85dbfc4c&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1647199&diff=357220 PMID:1647199 2008-02-08T00:54:48Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Williams, JS and Rosevear, PR''' (1991) A novel alpha-proton exchange reaction catalyzed by Escherichia coli methionyl-tRNA synthetase.''Biochemistry'' '''30''':6412-6</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The Escherichia coli truncated methionyl-tRNA synthetase (delta MTS) was shown to catalyze alpha-carbon hydrogen-deuterium exchange of L-selenomethionine, L-methionine, L-ethionine, and L-norleucine in the presence of deuterium oxide. The rate of alpha-proton exchange for L-methionine was shown to be linear with respect to delta MTS concentration. The exchange reaction showed saturation kinetics with apparent Km values of 21 and 4 mM in the absence and presence of saturating adenosine concentrations, respectively. As expected, delta MTS did not catalyze alpha-proton exchange of D-methionine since the enzyme has been shown to be specific for L-amino acids. In the absence of enzyme or in the presence of an equivalent concentration of Zn2+, no hydrogen-deuterium exchange was detected. The exchange reaction was not observed with L-methioninol, an analogue of L-methionine lacking the carboxylate group. These results suggest that the alpha-carboxylate group is a requirement for the delta MTS-catalyzed exchange reaction. The E. coli methionyl-tRNA synthetase (MTS) has previously been shown to be a zinc metalloprotein [Posorske, L. H., Cohn, M., Yanagisawa, N., & Auld, D. S. (1979) Biochim. Biophys. Acta 576, 128]. On the basis of the structural and mechanistic information available on MTS, we propose that the enzyme-bound zinc coordinates the carboxylate of the amino acid, while a base on the enzyme is responsible for exchange of the alpha-proton. The role of the enzyme-bound metal is to render the alpha-proton more acidic through coordination of the carboxylate group.(ABSTRACT TRUNCATED AT 250 WORDS)<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1647199 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241474' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R47aba85813b5a&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:2014166&diff=357219 PMID:2014166 2008-02-08T00:54:42Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Eriani, G, Dirheimer, G and Gangloff, J''' (1991) Cysteinyl-tRNA synthetase: determination of the last E. coli aminoacyl-tRNA synthetase primary structure.''Nucleic Acids Res.'' '''19''':265-9</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The gene coding for E. coli cysteinyl-tRNA synthetase (cysS) was isolated by complementation of a strain deficient in cysteinyl-tRNA synthetase activity at high temperature (43 degrees C). Sequencing of a 2.1 kbp DNA fragment revealed an open reading frame of 1383 bp coding for a protein of 461 amino acid residues with a Mr of 52,280, a value in close agreement with that observed for the purified protein, which behaves as a monomer. The sequence of CysRS bears the canonical His-Ile- Gly -His (HIGH) and Lys-Met-Ser-Lys-Ser (KMSKS) motifs characteristic of the group of enzymes containing a Rossmann fold; furthermore, it shows striking homologies with MetRS (an homodimer of 677 residues) and to a lesser extent with Ile-, Leu-, and ValRS (monomers of 939, 860, and 951 residues respectively). With its monomeric state and smaller size, CysRS is probably more closely related to the primordial aminoacyl-tRNA synthetase from which all have diverged.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2014166 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241473' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.N47aba852584d3&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1911947&diff=357218 PMID:1911947 2008-02-08T00:54:36Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Bailone, A, Sommer, S, Knezević, J and Devoret, R''' (1991) Substitution of UmuD' for UmuD does not affect SOS mutagenesis.''Biochimie'' '''73''':471-8</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || In order to study the role of UmuDC proteins in SOS mutagenesis, we have constructed new Escherichia coli K-12 strains to avoid i) over-production of Umu proteins, ii) the formation of unwanted mixed plasmid and chromosomal Umu proteins upon complementation. We inserted a mini-kan transposon into the umuD gene carried on a plasmid. The insertion at codon 24 ends protein translation and has a polar effect on the expression of the downstream umuC gene. We transferred umuD24 mutation to the E coli chromosome. In parallel, we subcloned umuD+ umuC+ or umuD' umuC+ genes into pSC101, a low copy number plasmid. In a host with the chromosomal umuD24 mutation, plasmids umuD+ umuC+ or umuD' umuC+ produced elevated resistance to UV light and increased SOS mutagenesis related to a gene dosage of about 3. UV mutagenesis was as high in umuD' umuC+ hosts devoid of UmuD+ protein as in umuD+ umuC+ hosts. UmuD' protein, the maturated form of UmuD, can substitute for UmuD in SOS mutagenesis.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1911947 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241472' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.E47aba84c9e37f&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1917941&diff=357217 PMID:1917941 2008-02-08T00:54:31Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Hinton, DM''' (1991) Transcription from a bacteriophage T4 middle promoter using T4 motA protein and phage-modified RNA polymerase.''J. Biol. Chem.'' '''266''':18034-44</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The bacteriophage T4 motA protein is required for transcription from T4 middle promoters. These promoters, which contain the Escherichia coli promoter consensus sequence at the -10 region (TATAAT) but a unique sequence centered at -30 ((a/t)(a/t)TGCTT(t/c)A) (Guild, N., Gayle, M., Sweeney, R., Hollingsworth, T., Modeer, T., and Gold, L. (1988) J. Mol. Biol. 199, 241-258), become active about 2 min after infection, a time when the host RNA polymerase has been modified by phage proteins. This paper shows that motA protein binds to a T4 middle promoter in vitro and that the addition of the motA protein allows in vitro transcription from this promoter by T4-modified RNA polymerase. The T4 motA gene was cloned into a multicopy plasmid that complemented T4 motA mutants in vivo. MotA protein, partially purified from cells containing a motA+ plasmid, specifically retarded the electrophoretic mobility of an oligomer containing the T4 middle promoter located 195 bases upstream of uvsX (PuvsX). RNA polymerase isolated from infected cells during T4 middle gene expression supported in vitro transcription from PuvsX only when fractions containing the motA protein were added. In contrast, unmodified host RNA polymerase catalyzed the synthesis of minor amounts of RNA from PuvsX, but this synthesis was not motA dependent. Thus, the in vitro transcription system described here provides the basis for a detailed study of the phage and host factors needed to regulate T4 middle gene expression.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1917941 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241471' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.C47aba846dc9c3&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1846148&diff=357216 PMID:1846148 2008-02-08T00:54:25Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Sobral, BW, Honeycutt, RJ and Atherly, AG''' (1991) The genomes of the family Rhizobiaceae: size, stability, and rarely cutting restriction endonucleases.''J. Bacteriol.'' '''173''':704-9</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The lack of high-resolution genetic or physical maps for the family Rhizobiaceae limits our understanding of this agronomically important bacterial family. On the basis of statistical analyses of DNA sequences of the Rhizobiaceae and direct evaluation by pulsed-field agarose gel electrophoresis (PFE), five restriction endonucleases with AT-rich target sites were identified as the most rarely cutting: AseI (5'-ATTAAT-3'), DraI (5'-TTTAAA-3'), SpeI (5'-ACTAGT-3'), SspI (5'-AATAAT-3'), and XbaI (5'-TCTAGA-3'). We computed the sizes of the genomes of Bradyrhizobium japonicum USDA 424 and Rhizobium meliloti 1021 by adding the sizes of DNA fragments generated by SpeI digests. The genome sizes of R. meliloti 1021 and B. japonicum USDA 424 were 5,379 +/- 282.5 kb and 6,195 +/- 192.4 kb, respectively. We also compared the organization of the genomes of free-living and bacteroid forms of B. japonicum. No differences between the PFE-resolved genomic fingerprints of free-living and mature (35 days after inoculation) bacteroids of B. japonicum USDA 123 and USDA 122 were observed. Also, B. japonicum USDA 123 genomic fingerprints were unchanged after passage through nodules and after maintenance on a rich growth medium for 100 generations. We conclude that large-scale DNA rearrangements are not seen in mature bacteroids or during free-living growth on rich growth media under laboratory conditions.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1846148 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241470' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Z47aba8410e785&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:2017367&diff=357215 PMID:2017367 2008-02-08T00:54:18Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Welsh, J and McClelland, M''' (1991) Genomic fingerprints produced by PCR with consensus tRNA gene primers.''Nucleic Acids Res.'' '''19''':861-6</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The polymerase chain reaction using only a single 'consensus' tRNA gene primer, or a pair of primers facing outward from tRNA genes, amplifies a set of DNA fragments in bacterial, plant and animal genomic DNAs. Presumably, these PCR fingerprints are mainly derived from the regions between closely linked tRNA genes. The pattern of the PCR products is determined by which genomes and which primer(s) are used. Genomic fingerprints are largely conserved within a species and, in bacteria, most products in the fingerprint are conserved between closely related species. Thus, PCR with tRNA gene consensus primers helps to identify species and genera.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2017367 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241469' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.M47aba83aa48fb&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1923811&diff=357214 PMID:1923811 2008-02-08T00:54:13Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Welsh, J and McClelland, M''' (1991) Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers.''Nucleic Acids Res.'' '''19''':5275-9</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Polymorphisms in genomic fingerprints generated by arbitrarily primed PCR (AP-PCR) can distinguish between slightly divergent strains of any organism. Single oligodeoxyribonucleotide (oligo) primers have been used to generate such fingerprints, with the same primer being present at the 5' end of both strands for every PCR product. We used three arbitrary oligos, individually and in pairs, to generate six different genomic fingerprints of the same mouse genomic DNAs. Fewer than half of the products in genomic fingerprints generated using the oligos in pairs were the same as those produced by AP-PCR using one of the three oligos alone. Thus, a few oligos could be used in a very large number of single and pairwise combinations, each producing a distinct AP-PCR fingerprint with the potential to identify new polymorphisms. For example, 50 oligos can be used in a matrix of pairwise combinations to produce 2,500 fingerprints, in which at least half the data can be expected to be unique to each pair. We demonstrate this principle by using two oligos, alone and together, to generate three sets of fingerprints and map thirteen polymorphisms in the C57BL/6J x DBA/2J set of recombinant inbred mice.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1923811 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241468' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.U47aba834e3651&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1886618&diff=357213 PMID:1886618 2008-02-08T00:54:07Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Nagano, Y, Matsuno, R and Sasaki, Y''' (1991) An essential gene of Escherichia coli that has sequence similarity to a chloroplast gene of unknown function.''Mol. Gen. Genet.'' '''228''':62-4</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The dedB gene of Escherichia coli has sequence similarity to the zfpA gene of the chloroplast chromosome. The functions of dedB and zfpA are unknown. We constructed derivatives of temperature-sensitive polA strains into whose chromosomes a plasmid containing the disrupted dedB gene was integrated by homologous recombination. These strains contained normal and disrupted dedB genes in their chromosomes. We then selected plasmid-segregated strains and found no cells containing the disrupted dedB gene, indicating that disruption of the dedB gene was lethal in polA strains of E. coli.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1886618 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241467' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47aba82f11832&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1376322&diff=357212 PMID:1376322 2008-02-08T00:54:01Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Deckers-Hebestreit, G, Simoni, RD and Altendorf, K''' (1992) Influence of subunit-specific antibodies on the activity of the F0 complex of the ATP synthase of Escherichia coli. I. Effects of subunit b-specific polyclonal antibodies.''J. Biol. Chem.'' '''267''':12364-9</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Incubation of F1-stripped everted membrane vesicles with antibodies against subunit b of the ATP synthase from Escherichia coli resulted in an inhibition of the binding of F1 to F0, whereas the proton translocation remained unaffected. Incubation of unstripped everted membrane vesicles with anti-b antibodies resulted in a partial loss of F1, and the remaining membrane-bound ATP-hydrolyzing activity is uncoupled from proton translocation. Similar results were obtained when F(ab')2 or Fab fragments were used. The immunoblot analysis of truncated b' subunits different in length showed that the antigenic determinants are located in the carboxyl-terminal half of the polypeptide chain.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1376322 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241466' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.L47aba82955cb4&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1376323&diff=357211 PMID:1376323 2008-02-08T00:53:55Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Deckers-Hebestreit, G and Altendorf, K''' (1992) Influence of subunit-specific antibodies on the activity of the F0 complex of the ATP synthase of Escherichia coli. II. Effects of subunit c-specific polyclonal antibodies.''J. Biol. Chem.'' '''267''':12370-4</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || After incubation of F1-stripped everted membrane vesicles with antibodies against subunit c of the ATP synthase of Escherichia coli the proton translocation through the open F0 channel was blocked. Rebinding of F1 to those vesicles is affected by the antibody concentration used. In general, the use of F(ab')2 or Fab fragments prepared from anti-c antibodies gave similar results. However, using Fab fragments a higher amount of antigenic binding sites was necessary to block the F0 complex completely, whereas extremely low amounts of Fab fragments were necessary to inhibit the binding of F1. This can be explained by an antigenic determinant of subunit c, which is only accessible to the smaller Fab fragments with a molecular mass of approximately 50,000. Incubation of F1-containing everted membranes with anti-c antibodies showed that the binding of the antibodies resulted in a displacement of F1, while simultaneously the proton translocation through F0 has been blocked. Such a displacement can only be observed after incubation with IgG molecules or F(ab')2 fragments. Fab fragments were not able to displace the F1 part, indicating that the ability of antibodies and F(ab')2 fragments to produce cross-links is responsible for the loss of F1 from the membranes.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1376323 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241465' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.J47aba8239af1a&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1608464&diff=357210 PMID:1608464 2008-02-08T00:53:49Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Chothia, C''' (1992) Proteins. One thousand families for the molecular biologist.''Nature'' '''357''':543-4</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1608464 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241464' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.N47aba81d84558&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1538746&diff=357209 PMID:1538746 2008-02-08T00:53:44Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''McClelland, M and Bhagwat, AS''' (1992) Biased DNA repair.''Nature'' '''355''':595-6</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1538746 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241463' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.B47aba817cdf2e&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1579457&diff=357208 PMID:1579457 2008-02-08T00:53:38Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Bhagwat, AS and McClelland, M''' (1992) DNA mismatch correction by Very Short Patch repair may have altered the abundance of oligonucleotides in the E. coli genome.''Nucleic Acids Res.'' '''20''':1663-8</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || A base mismatch correction process in E. coli K-12 called Very Short Patch (VSP) repair corrects T:G mismatches to C:G when found in certain sequence contexts. Two of the substrate mismatches (5'-CTWGG/3'-GGW'CC; W = A or T) occur in the context of cytosine methylation in DNA and reduce the mutagenic effects of 5-methylcytosine deamination to thymine. However, VSP repair is also known to repair T:G mismatches that are not expected to arise from 5-methylcytosine deamination (example--CTAG/GGT-C). In these cases, if the original base pair were a T:A, VSP repair would cause a T to C transition. We have carried out Markov chain analysis of an E. coli sequence database to determine if repair at the latter class of sites has altered the abundance of the relevant tetranucleotides. The results are consistent with the prediction that VSP repair would tend to deplete the genome of the 'T' containing sequences (example--CTAG), while enriching it for the corresponding 'C' containing sequences (CCAG). Further, they provide an explanation for the known scarcity of CTAG containing restriction enzyme sites among the genomes of enteric bacteria and identify VSP repair as a force in shaping the sequence composition of bacterial genomes.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1579457 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241462' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.N47aba811e353c&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1406262&diff=357207 PMID:1406262 2008-02-08T00:53:32Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Maskell, D''' (1992) Protein sequence from downstream of Escherichia coli galK is homologous with galM from other organisms.''Mol. Microbiol.'' '''6''':2211</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1406262 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241461' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.K47aba80c35ae6&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1317854&diff=357206 PMID:1317854 2008-02-08T00:53:26Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Ta, DT and Vickery, LE''' (1992) Cloning, sequencing, and overexpression of a [2Fe-2S] ferredoxin gene from Escherichia coli.''J. Biol. Chem.'' '''267''':11120-5</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Escherichia coli contains a soluble, [2Fe-2S] ferredoxin of unknown function (Knoell, H.-E., and Knappe, J. (1974) Eur. J. Biochem. 50, 245-252). Using antiserum to the purified protein to screen E. coli genomic expression libraries, we have cloned a gene (designated fdx) encoding this protein. The DNA sequence of the gene predicts a polypeptide of 110 residues after removal of the initiator methionine (polypeptide M(r) = 12,186, holoprotein M(r) = 12,358). The deduced amino acid sequence is strikingly similar to those of the ferredoxins found in animal mitochondria which function with cytochrome P450 enzymes and to the ferredoxin from Pseudomonas putida which functions with P450cam. The overall sequence identity is approximately 36% when compared with human mitochondrial and P. putida ferredoxins, and the identities include 4 cysteine residues proposed to coordinate the iron cluster. The protein was overproduced approximately 500-fold using an expression plasmid, and the holoprotein was assembled and accumulated in amounts exceeding 30% of the total cell protein. The overexpressed ferredoxin exhibits absorption, circular dichroism, and electron paramagnetic resonance spectra closely resembling those of the animal ferredoxins and P. putida ferredoxin.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1317854 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241460' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.A47aba8067ac01&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1512212&diff=357205 PMID:1512212 2008-02-08T00:53:20Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Ta, DT, Seaton, BL and Vickery, LE''' (1992) Localization of the ferredoxin (fdx) gene on the physical map of the Escherichia coli chromosome.''J. Bacteriol.'' '''174''':5760-1</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1512212 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241459' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R47aba800ba9b2&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1644192&diff=357204 PMID:1644192 2008-02-08T00:53:15Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Siebert, M, Bechthold, A, Melzer, M, May, U, Berger, U, Schröder, G, Schröder, J, Severin, K and Heide, L''' (1992) Ubiquinone biosynthesis. Cloning of the genes coding for chorismate pyruvate-lyase and 4-hydroxybenzoate octaprenyl transferase from Escherichia coli.''FEBS Lett.'' '''307''':347-50</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Chorismate pyruvate-lyase activity was detected in extracts of Escherichia coli. 4-Hydroxybenzoate was identified as the product of the enzymatic reaction by chemical derivatization and GC-MS analysis. The ubiC gene, coding for the chorismate pyruvate-lyase, was cloned and sequenced. The molecular weight of the gene product was calculated as 18,776 Da and confirmed by expression of the protein in E. coli minicells. The ubiA gene, coding for the 4-hydroxybenzoate octaprenyl transferase, was identified by sequence homology and complementation of a ubiA- strain. It is located directly downstream of ubiC in a typical operon structure.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1644192 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241458' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.G47aba7fb0e04a&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1567861&diff=357203 PMID:1567861 2008-02-08T00:53:09Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Hou, YM and Schimmel, P''' (1992) Novel transfer RNAs that are active in Escherichia coli.''Biochemistry'' '''31''':4157-60</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || Many of the mammalian mitochondrial tRNAs contain significant nucleotide deletions in the dihydrouridine (D) stem or T psi C stem, so that they cannot fold into the canonical cloverleaf structure. This suggests that alternative forms and shapes are possible for a mitochondrial tRNA that functions in the specialized translational apparatus of the mammalian mitochondria. The question of whether significant structural alterations may be accommodated by a bacterial protein synthesis machinery, such as in Escherichia coli, is unanswered. In this work, all but ten positions in the gene for the 76-nucleotide coding sequence of an E. coli amber suppressor tRNA were permuted and screened for biological activity in vivo. Sequence analysis of a collection of biologically active variants established that many have unusual structures that include base-pair mismatches in helical stems, substitutions of normally conserved bases, and deletions. Independent mutations were obtained that weaken base pairs or tertiary interactions that normally stabilize the coaxial stacking of the D and anticodon stems, suggesting that the translational apparatus can accommodate considerable flexibility in this part of the molecule. The results demonstrate the capacity of the bacterial protein synthetic apparatus to accommodate altered tRNA structures that are not represented by any naturally occurring tRNAs.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1567861 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241457' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.L47aba7f552fa8&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1420150&diff=357202 PMID:1420150 2008-02-08T00:53:03Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Hou, YM and Schimmel, P''' (1992) Functional compensation of a recognition-defective transfer RNA by a distal base pair substitution.''Biochemistry'' '''31''':10310-4</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || A single G3:U70 base pair in the acceptor helix is the major determinant of alanine acceptance in alanine transfer RNAs. Transfer of this base pair into other transfer RNAs confers alanine acceptance. A G3:C70 substitution eliminates alanine acceptance in vivo and in vitro. In this work, a population of mutagenized G3:C70 alanine tRNA amber suppressors was subjected to a selection for mutations that compensate for the inactivating G3:C70 substitution. No compensatory mutations located in the acceptor helix were obtained. Instead, a U27:U43 substitution that replaced the wild-type C27:G43 in the anticodon stem created a U27:U43/G3:C70 mutant alanine tRNA that inserts alanine at amber codons in vivo. The U27:U43 substitution is at a location where previous footprinting work established an RNA-protein contact. Thus, this mutation may act by functionally coupling a distal part of the tRNA structure to the active site.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1420150 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241456' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Z47aba7ef98fb4&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1372677&diff=357201 PMID:1372677 2008-02-08T00:52:58Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Tétart, F and Bouché, JP''' (1992) Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules.''Mol. Microbiol.'' '''6''':615-20</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || We show that the 53-nucleotide RNA molecule encoded by gene dicF blocks cell division in Escherichia coli by inhibiting the translation of ftsZ mRNA. Such a role for dicF had been predicted on the basis of the complementarity of DicF RNA with the ribosome-binding region of the ftsZ mRNA. An analysis of ftsZ expression at its chromosomal locus, and of an ftsZ-lacZ translational fusion controlled by promoters ftsZ1p and ftsZ2p only, indicates that ftsZ is not autoregulated. Partial inhibition of FtsZ synthesis leads to increased cell size. However, the number of FtsZ molecules per cell can be reduced threefold without affecting the division rate significantly. Our results suggest that septation is not triggered by a fixed number of newly synthesized FtsZ molecules per cell.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1372677 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241455' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.F47aba7e9d4db1&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1552861&diff=357200 PMID:1552861 2008-02-08T00:52:52Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Tétart, F, Albigot, R, Conter, A, Mulder, E and Bouché, JP''' (1992) Involvement of FtsZ in coupling of nucleoid separation with septation.''Mol. Microbiol.'' '''6''':621-7</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The cell-cycle parameters of an Escherichia coli strain expressing essential division gene ftsZ at one-fifth of its normal level, because of antisense regulation by DicF RNA, have been analysed. Inhibition of FtsZ expression affects neither the generation time nor the replication initiation mass, the C period, or the constriction period, but it does dramatically retard the initiation of constriction relative to replication termination. Separation of the nucleoids is equally postponed, indicating that division is not coupled to termination of replication, but to partitioning. The severe inhibition of nucleoid separation by DicF RNA, and its suppression by overproduction of FtsZ, suggest a role for FtsZ in the control of separation, and consequently in the coupling of separation and division. We suggest that the normal pattern of nucleoid separation previously found in cells deficient in ftsZ function was a consequence of the loss of a negative effect exerted by FtsZ on separation. In agreement with this view, we find that nucleoid separation is temporarily inhibited after arrest of FtsZ synthesis, but is later resumed as FtsZ is further diluted into the elongating filaments.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1552861 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241454' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.N47aba7e426472&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1624437&diff=357199 PMID:1624437 2008-02-08T00:52:46Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''el-Hajj, HH, Wang, L and Weiss, B''' (1992) Multiple mutant of Escherichia coli synthesizing virtually thymineless DNA during limited growth.''J. Bacteriol.'' '''174''':4450-6</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The dut gene of Escherichia coli encodes deoxyuridine triphosphatase, an enzyme that prevents the incorporation of dUTP into DNA and that is needed in the de novo biosynthesis of thymidylate. We produced a conditionally lethal dut(Ts) mutation and isolated a phenotypic revertant that had a mutation in an unknown gene tentatively designated dus (for dut suppressor). The dus mutation restored the ability of the dut mutant to grow at 42 degrees C without restoring its enzymatic activity or thymidylate independence. A strain was constructed bearing, in addition to these mutations, ones affecting the following genes and their corresponding products: ung, which produces uracil-DNA N-glycosylase, a repair enzyme that removes uracil from DNA; deoA, which produces thymidine (deoxyuridine) phosphorylase, which would degrade exogenous deoxyuridine; and thyA, which produces thymidylate synthase. When grown at 42 degrees C in minimal medium containing deoxyuridine, the multiple mutant displayed a 93 to 96% substitution of uracil for thymine in new DNA. Growth stopped after the cellular DNA had increased 1.6- to 1.9-fold and the cell mass had increased 1.7- to 2.7-fold, suggesting a general failure of macromolecular biosynthesis. DNA hybridization confirmed that the uracil-containing DNA was chromosomal and that new rounds of initiation must have occurred during its synthesis.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1624437 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241453' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R47aba7de6bacc&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1324907&diff=357198 PMID:1324907 2008-02-08T00:52:40Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Wang, L and Weiss, B''' (1992) dcd (dCTP deaminase) gene of Escherichia coli: mapping, cloning, sequencing, and identification as a locus of suppressors of lethal dut (dUTPase) mutations.''J. Bacteriol.'' '''174''':5647-53</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || In Escherichia coli, most of the dUMP that is used as a substrate for thymidylate synthetase is generated from dCTP through the sequential action of dCTP deaminase and dUTPase. Some mutations of the dut (dUTPase) gene are lethal even when the cells are grown in the presence of thymidine, but their lethality can be suppressed by extragenic mutations that can be produced by transposon insertion. Six suppressor mutations were tested, and all were found to belong to the same complementation group. The affected gene was cloned, it was mapped by hybridization with a library of recombinant DNA, and its nucleotide sequence was determined. The gene is at 2,149 kb on the physical map. Its product, a 21.2-kDa polypeptide, was overproduced 1,000-fold via an expression vector and identified as dCTP deaminase, the enzyme affected in previously described dcd mutants. Null mutations in dcd probably suppress the lethality of dut mutations by reducing the accumulation of dUTP, which would otherwise lead to the excessive incorporation of uracil into DNA.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1324907 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241452' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.O47aba7d8b1f8b&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1549561&diff=357197 PMID:1549561 2008-02-08T00:52:35Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Miller, WT and Schimmel, P''' (1992) A retroviral-like metal binding motif in an aminoacyl-tRNA synthetase is important for tRNA recognition.''Proc. Natl. Acad. Sci. U.S.A.'' '''89''':2032-5</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || The gag genes of retroviruses encode nucleocapsid proteins that package genomic RNA and are essential for viral infectivity. These RNA binding proteins have a Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys zinc binding motif that is distinct from the typical zinc-finger motif Cys-Xaa2-Cys-Xaa12-14-His-Xaa2-His that is found in some transcriptional activators. Escherichia coli alanyl-tRNA synthetase contains a zinc-binding Cys-Xaa2-Cys-Xaa6-His-Xaa2-His motif that resembles that of retroviral nucleic acid binding proteins. We show here that, for alanyl-tRNA synthetase, the metal bound at the retroviral-like metal binding motif is important specifically for tRNA recognition and not for amino acid activation. Moreover, the enzyme-tRNA interaction is strongly dependent on the geometry of metal coordination to the protein. These and additional experiments collectively suggest a role for the retroviral-like metal binding motif in RNA recognition and, further, raise the possibility that the protein-bound metal itself participates in an RNA interaction.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1549561 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241451' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47aba7d304821&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61 https://ecoliwiki.org/colipedia/index.php?title=PMID:1379318&diff=357196 PMID:1379318 2008-02-08T00:52:29Z

<p>165.91.51.61: New PMID: Page!</p> <hr /> <div><protect><br /> {{RightTOC}}<br /> <br /> <span style = 'font-size: large'> '''Miller, WT and Schimmel, P''' (1992) A metal-binding motif implicated in RNA recognition by an aminoacyl-tRNA synthetase and by a retroviral gene product.''Mol. Microbiol.'' '''6''':1259-62</span><br /> <br /> {|{{Prettytable}} align = 'center' width= '70%'<br /> |-<br /> |{{TableHeadingColor}} |'''Abstract''' || A randomly generated mutation in Escherichia coli alanine tRNA synthetase compensates for a mutation in its cognate tRNA. The enzyme's mutation occurs next to a Cys-X2-Cys-X6-His-X2-His metal-binding motif that is distinct from the zinc finger motif found in some DNA-binding proteins. Instead, the synthetase's metal binding domain resembles the Cys-X2-Cys-X4-His-X4-Cys metal-binding domain of the gag gene product of retroviruses. For Ala-tRNA synthetase, the metal bound at the Cys-His motif is important specifically for the tRNA-dependent step of catalysis, and the enzyme-tRNA interaction is dependent on the geometry of metal co-ordination to the enzyme. These data, and the demonstrated sensitivity of RNA packaging to mutations in the metal-binding domain of the gag gene product of retroviruses, suggest that an aminoacyl-tRNA synthetase and retroviruses have adopted a related metal-binding motif for RNA recognition.<br /> </noinclude><br /> |-<br /> |{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1379318 PubMed]<br /> |}<br /> </protect><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 /> <protect><br /> <br /> {|class = 'sortable' {{Prettytable}} id='241450' <br /> |- {{table heading style}}<br /> !Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status<br /> |-class='sortbottom'<br /> |[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.T47aba7cd4a251&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||<br /> |}<br /> </protect><br /> <br /> ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==<br /> {{LitLinks}}<br /> <br /> ==References==<br /> {{RefHelp}}<br /> <references/></div>

165.91.51.61