dinB:Expression: Difference between revisions

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==Overview==
===Overview===
{{Expression_overview_placeholder}}
{{Expression_overview_placeholder}}
==Cellular Levels==
{{BacktoTop}}
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!|Molecule!!Organism or Strain!!Value!!Units!!Experimental Conditions!!Assay used!!Notes!!Reference(s)
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Protein
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''E. coli'' K-12 MG1655
|
47
|
molecules/cell/generation
|
*Medium: MOPS Complete 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
|
PMID: 24766808
|-
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Protein
|
''E. coli'' K-12 MG1655
|
20
|
molecules/cell/generation
|
*Medium: MOPS Minimal 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
|
PMID: 24766808
|-
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Protein
|
''E. coli'' K-12 MG1655
|
13<sup>a</sup>
|
molecules/cell/generation
|
*Medium: MOPS Complete without Methionine 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
Low confidence in the sequencing data set.
|
PMID: 24766808
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===Notes===
==Transcription and Transcriptional Regulation==
==Transcription and Transcriptional Regulation==
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{{BacktoTop}}
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[[:Category:Txn_unit:dinB|dinB]]  
[[:Category:Txn_unit:dinB|dinB yafNOP]]  
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{{expression_transcription_help}}
 
<!--Transcription_notes--></protect>
<!--Transcription_notes--></protect>
===Notes===
===Notes===
{{Expression_transcription_placeholder}}
Transcription is repressed by LexA <ref name='PMID:16196125'/>
Transcription is repressed by LexA <ref name='PMID:16196125'/>
Transcription in stationary phase is RpoS-dependent <ref name='PMID:14617178'/>
Transcription in stationary phase is RpoS-dependent <ref name='PMID:14617178'/>


==Translation and Regulation of Translation==
==Translation and Regulation of Translation==
{{BacktoTop}}
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<protect>{{GBrowseFigureByCoord|250878|250918|ecoli|MG1655|Genes_unlabeled+DNA_unlabeled|400|{{Nterm_closeup}} }}
<protect><gbrowseImage>
name=NC_000913:250878..250918
source=MG1655
type=Gene+DNA_+Protein
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===Notes===
===Notes===
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===Notes===
===Notes===
{{Expression_turnover_placeholder}}
DinB protein levels are GroEL-dependent <ref name='PMID:15629916'/>


==Experimental==
==Experimental==
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<big>'''Expression Studies'''</big>
<big>'''Expression Studies'''</big>
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microarray  
microarray
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0231 EcoliGenExpDB:b0231] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://genexpdb.ou.edu/index.php?query=b0231 GenExpDB:b0231] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
Summary of data for dinB from multiple microarray studies   
Summary of data for dinB from multiple microarray studies   
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microarray
|
PMID: 11333217
|
UV induction
|-
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microarray
|
[[geoprofiles:b0231|GEO Profiles:b0231]] ([[Gene_Expression_Omnibus_%28GEO%29|EcoliWiki Page]])
|
NCBI GEO profiles for ''dinB''
 
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<big>'''Expression Resources'''</big>
<big>'''Expression Resources'''</big>
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|
GFP Fusion
|
Intergenic region (250744..250966) fused to <i>gfpmut2</i>.
|
[http://www.openbiosystems.com/GeneExpression/Non-Mammalian/Bacteria/EcoliPromoters/ OpenBioSystems][[Category:Genes in OpenBioSystems with Promoter Fusions]]
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GFP fusion described in Zaslaver, <i>et al.</i><br />Plate:109-AZ12; Well:G7<ref name="PMID: 16862137" />
 
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<protect><!--Expression_experimental_notes--></protect>
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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6115 EcoCyc:G6115] 
EcoCyc:G6115
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2935 EchoBASE:EB2935] 
EchoBASE:EB2935
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0231 EcoliGenExpDB:b0231]
[http://chase.ou.edu/macro/searchlink.php?bnum=b0231 EcoliGenExpDB:b0231]
|
|
   
   
|-
|-
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[[EcoGene]]
|
EcoGene:EG13141
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120002735
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[ASAP]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13141 EcoGene:EG13141] 
ASAP:ABE-0000789
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<protect><!--Accessions_notes--></protect>
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===Notes===
===Notes===
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<noinclude>
<noinclude>
==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Txn_unit:dinB]]
[[Category:Txn_unit:dinB]]

Latest revision as of 19:44, 21 July 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Overview Transcription Translation Turnover Experimental Links References Suggestions

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

47

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID:24766808[1]

Protein

E. coli K-12 MG1655

20

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID:24766808[1]

Protein

E. coli K-12 MG1655

13a

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID:24766808[1]

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

dinB yafNOP

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Figure courtesy of RegulonDB


Notes

Transcription is repressed by LexA [2] Transcription in stationary phase is RpoS-dependent [3]

Translation and Regulation of Translation

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<gbrowseImage> name=NC_000913:250878..250918 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.


Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

DinB protein levels are GroEL-dependent [4]

Experimental

[back to top]


Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GenExpDB:b0231 (EcoliWiki Page)

Summary of data for dinB from multiple microarray studies

microarray

PMID:11333217[5]

UV induction

microarray

GEO Profiles:b0231 (EcoliWiki Page)

NCBI GEO profiles for dinB

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (250744..250966) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:G7[6]

edit table

<protect>

Notes

Accessions Related to dinB Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:G6115

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2935

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0231

EcoGene

EcoGene:EG13141

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002735

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000789

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 Li, GW et al. (2014) Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157 624-35 PubMed
  2. ↑ Kenyon, CJ & Walker, GC (2005) DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. 1980. DNA Repair (Amst.) 4 1049-53 PubMed
  3. ↑ Layton, JC & Foster, PL (2003) Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli. Mol. Microbiol. 50 549-61 PubMed
  4. ↑ Layton, JC & Foster, PL (2005) Error-prone DNA polymerase IV is regulated by the heat shock chaperone GroE in Escherichia coli. J. Bacteriol. 187 449-57 PubMed
  5. ↑ Courcelle, J et al. (2001) Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics 158 41-64 PubMed
  6. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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