EcoliWiki - User contributions [en]

PMID:15262935

2007-08-06T22:15:24Z

Kmwassarman: New PMID: Page!

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 '''Trotochaud, AE and Wassarman, KM''' (2004) 6S RNA function enhances long-term cell survival.''J. Bacteriol.'' '''186''':4978-85

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|{{TableHeadingColor}} |'''Abstract''' || 6S RNA was identified in Escherichia coli >30 years ago, but the physiological role of this RNA has remained elusive. Here, we demonstrate that 6S RNA-deficient cells are at a disadvantage for survival in stationary phase, a time when 6S RNA regulates transcription. Growth defects were most apparent as a decrease in the competitive fitness of cells lacking 6S RNA. To decipher the molecular mechanisms underlying the growth defects, we have expanded studies of 6S RNA effects on transcription. 6S RNA inhibition of sigma(70)-dependent transcription was not ubiquitous, in spite of the fact that the vast majority of sigma(70)-RNA polymerase is bound by 6S RNA during stationary phase. The sigma(70)-dependent promoters inhibited by 6S RNA contain an extended -10 promoter element, suggesting that this feature may define a class of 6S RNA-regulated genes. We also discovered a secondary effect of 6S RNA in the activation of sigma(S)-dependent transcription at several promoters. We conclude that 6S RNA regulation of both sigma(70) and sigma(S) activities contributes to increased cell persistence during nutrient deprivation.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15262935 PubMed]
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==Significance {{HelpIcon|Help:Literature}} ==
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== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
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==Annotations {{HelpIcon|Help:Literature}}==
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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==References==
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<references/>

PMID:2579059

2007-08-06T22:14:42Z

Kmwassarman: New PMID: Page!

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 '''Lee, CA, Fournier, MJ and Beckwith, J''' (1985) Escherichia coli 6S RNA is not essential for growth or protein secretion.''J. Bacteriol.'' '''161''':1156-61

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|{{TableHeadingColor}} |'''Abstract''' || The function of the stable 6S RNA of Escherichia coli is not known. Recently, it was proposed that the 6S RNA is a component of a bacterial signal recognition particle required for protein secretion. To test this proposal, we isolated a mutant that lacks the 6S RNA. Studies of the mutant show that the 6S RNA is not essential for growth or for protein secretion. The gene for the 6S RNA (ssr) maps near serA at 63 min on the E. coli genetic map.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2579059 PubMed]
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==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
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{|class = 'sortable' {{Prettytable}} id='220145'
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.T46b79d51cd84a&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==References==
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<references/>

ssrS:Gene

2007-08-06T22:14:16Z

Kmwassarman: edited by Kmwassarman via TableEdit

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{{Tab|Quickview|ssrS}}{{Tab On|Gene|ssrS}}{{Tab|Gene Product(s)|ssrS}}{{Tab|Expression|ssrS}}{{Tab|Evolution|ssrS}}{{Tab|On One Page|ssrS}}{{TabsBottom}}
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|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
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==Nomenclature==
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!{{table_heading_style}} |Standard name
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''ssrS''
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!{{table_heading_style}} |Mnemonic
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!{{table_heading_style}} |Synonyms
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''ECK2906, b2911, JWR0067, ssr''<ref name='LIB:Riley_2006'/>
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===Notes===

==Location(s) and DNA Sequence==
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{|class = 'sortable' {{Prettytable}} id='142358'
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
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65.82 minutes 
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MG1655: 3054005..3054187 {{GBrowseFigureByCoord|3053005|3055187|ecoli|MG1655}}
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG30099 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3053005..3055187 GBrowse(MG1655)]

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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3054005..3054187&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=EG30099 EcoCyc Sequence Dump]
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W3110
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W3110: 3054639..3054821 {{GBrowseFigureByCoord|3053639|3055821|ecoli_W3110|W3110}}
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3053639..3055821 GBrowse(W3110)]
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3054639..3054821&plugin_action=Go FASTA Dump]
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{{Gene_location_help}}
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===Notes===

==Sequence Features==
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{|class = 'sortable' {{Prettytable}} id='142359'
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!Feature type!!Location!!Description
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====Notes====

==Alleles and Phenotypes==
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{|class = 'sortable' {{Prettytable}} id='142360'
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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ΔssrS (Keio:)
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deletion
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deletion
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[[PMID:16738554]]<ref name=PMID:16738554/>
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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ssrS1
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insertion after nt 84
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Growth Phenotype
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long term growth defect
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[[PMID:2579059]]<ref name=PMID:2579059/>
[[PMID:15262935]]<ref name=PMID:15262935/>
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original allele name: ssr1
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===Notes===

==Genetic Resources==
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{|class = 'sortable' {{Prettytable}} id='142361'
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!Resource!!Resource Type!!Source!!Notes/Reference
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Plasmid clone
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
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[[PMID:16769691]]<ref name=PMID:16769691/>

Status:

Primer 1:

Primer 2:
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[[recD:Gene|recD1901::Tn10]]
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Linked marker
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CAG12135 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40106 CGSC7429]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
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[[speA:Gene|speA210::Tn10]]
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Linked marker
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CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zgd-210::Tn10, zgf-210::Tn10
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===Notes===

==Accessions in Other Databases==
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{|class = 'sortable' {{Prettytable}} id='142362'
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!Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG30099 EcoCyc:EG30099]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4262 EchoBASE:EB4262]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2911 EcoliGenExpDB:b2911]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG30099 EcoGene:EG30099]
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{{Gene_accessions_help}}
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===Notes===

==Links==
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!Name!!URL!!Comments
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==References==
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<references/>
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]