recB:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2816, b2820, JW2788, rorA, ior''<ref name='LIB:Riley_2006'/>
''ECK2816, b2820, JW2788, rorA, ior''<ref name='LIB:Riley_2006'/>, ior''


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9e70cd514e"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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W3110: 2954659..2951117<br /><gbrowseImage>
W3110: 2954659..2951117<br /><gbrowseImage>
name=AC_000091:2951117..2954659
name=NC_007779:2951117..2954659
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|2950117|2955659|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2950117|2955659|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|2951117|2954659|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2951117|2954659|FASTA Dump}}  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="Y46a9e70d912fc"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a9e70d912fc"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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****************************************************************************************** -->{{Gene_alleles_help}}
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{| {{Prettytable}} id="L46a9e70dd82cb"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="L46a9e70dd82cb"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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&Delta;recB (Keio:JW2788)
''recB(del)'' (Keio:JW2788)
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deletion
deletion
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PMID:16738554
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108463 CGSC10182]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108463 CGSC10182]<ref name='LIB:cgsc'/>  
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''&#916;recB745::kan''
''recB745(del)''::kan
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recB(del) in MDS42
recB in [[MDS42]]
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deletion
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fig. 2  
fig. 2  
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recB
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deletion
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Sensitivity to
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decreases sensitivity to [[Bicyclomycin]]
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PMID:21357484
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fig 2
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''nrdA101 recB(del)''
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''recB'' function is deactivated
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Rate of DNA replication
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When exposed to extreme temperatures the rate of transcription is slightly under restrictive conditions
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PMID:21441507
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See Figure 2
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''recB268''::Tn''10''
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Tn''10'' was inserted into the ''recB'' gene at the allele 268.
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Growth Phenotype
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the rate of growth was significantly decreased.
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PMID:9973363
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See figure 1.  The strain background is Hfr3000; called '3000HfrH' in the paper. 
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SMR6039 ''recB(del)''::Kan
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Deletion
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SOS response
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Decrease in spontaneous SOS-induction defective
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PMID:23224554
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Parent Strain: SMR6039
Experimental Strain: SMR16024
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The mutation caused a defect in Spontaneous SOS-Induction. See table S7 for a summary of experimental results. 


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{|   id="P4e04c225d976d"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P4e04c225d976d"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=459 Genobase]
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=459 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:3G11|3G11]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=460 Genobase]
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PMID:3038334  
PMID:3038334  
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est. P1 cotransduction: 99% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 99% <ref name='LIB:Nichols_linked_Tn'/>  
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[[:Category:Kohara_Phage:3G11|3G11]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=460 Genobase]
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PMID:3038334


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{|   id="J46a9e70f37d7f"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9e70f37d7f"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10824 EcoCyc:EG10824]
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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=EB0817 EchoBASE:EB0817]
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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=b2820 EcoliGenExpDB:b2820]
EcoCyc:EG10824
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
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[http://BioCyc.org/ECOL199310/new-image?object=C3414 ECOL199310CYC:C3414]
EcoGene:EG10824
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10824 EcoGene:EG10824]
RegulonDB:ECK120000815
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=RECB ECOO157CYC:RECB]
[http://www.ncbi.nlm.nih.gov/gene?term=947286 GeneID:947286]
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Escherichia coli str. K-12 substr. MG1655
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/311 CGSC:311]
EchoBASE:EB0817
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009249&formSubmitReturn=1 ASAP:ABE-0009249]
ASAP:ABE-0009249
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:44, 19 September 2013

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

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

recB

Mnemonic

Recombination

Synonyms

ECK2816, b2820, JW2788, rorA, ior[1], ior

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

63.59 minutes 

MG1655: 2954025..2950483
<gbrowseImage> name=NC_000913:2950483..2954025 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2850622..2847080
<gbrowseImage> name=NC_012967:2847080..2850622 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2837631..2841173
<gbrowseImage> name=NC_012759:2837631..2841173 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2954659..2951117
<gbrowseImage> name=NC_007779:2951117..2954659 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3047895..3044353
<gbrowseImage> name=NC_010473:3044353..3047895 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

2950486

Edman degradation

PMID:1618858[2]


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

recB(del) (Keio:JW2788)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10182[4]

recB::Tn5KAN-I-SceI (FB20945)

Insertion at nt 2423 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20945

contains pKD46

recB::Tn5KAN-I-SceI (FB20946)

Insertion at nt 2423 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20946

does not contain pKD46

recB21

CGSC:4677

recB270(ts)

temperature sensitive

CGSC:8994

recB1067(D1067A)

PMID:9790841[6]

CGSC:71962

recB1080(D1080A)

PMID:11532156[7]

CGSC:72006

recB1082(K1082Q)

PMID:9790841[6]

CGSC:72009

recB60

CGSC:84445

recB745(del)::kan

PMID:16738554[3]

CGSC:102622

recB in MDS42

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21183718[8]

fig. 2

recB

deletion

Sensitivity to

decreases sensitivity to Bicyclomycin

PMID:21357484[9]

fig 2

nrdA101 recB(del)

recB function is deactivated

Rate of DNA replication

When exposed to extreme temperatures the rate of transcription is slightly under restrictive conditions

PMID:21441507[10]

See Figure 2

recB268::Tn10

Tn10 was inserted into the recB gene at the allele 268.

Growth Phenotype

the rate of growth was significantly decreased.

PMID:9973363[11]

See figure 1. The strain background is Hfr3000; called '3000HfrH' in the paper.

SMR6039 recB(del)::Kan

Deletion

SOS response

Decrease in spontaneous SOS-induction defective

PMID:23224554[12]

Parent Strain: SMR6039 Experimental Strain: SMR16024

The mutation caused a defect in Spontaneous SOS-Induction. See table S7 for a summary of experimental results.

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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2788

Plasmid clone

Shigen

PMID:16769691[13]

Status:Clone OK

Primer 1:GCCAGTGATGTCGCCGAGACACT

Primer 2:CCgGCCTCCTCCAGGGTCATACC

10B6

Kohara Phage

Genobase

PMID:3038334[14]

3G11

Kohara Phage

Genobase

PMID:3038334[14]

fucP3072::Tn10

Linked marker

CAG12079 = CGSC7427[4]

est. P1 cotransduction: 52% [15]
Synonyms:fuc-3072::Tn10

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[4]

est. P1 cotransduction: 99% [15]

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Notes

Accessions in Other Databases

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

Database Accession Notes

EcoCyc

EcoCyc:EG10824

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10824

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000815

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947286

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0817

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009249

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Masterson, C et al. (1992) Reconstitution of the activities of the RecBCD holoenzyme of Escherichia coli from the purified subunits. J. Biol. Chem. 267 13564-72 PubMed
  3. ↑ 3.0 3.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 6.0 6.1 Yu, M et al. (1998) Identification of the nuclease active site in the multifunctional RecBCD enzyme by creation of a chimeric enzyme. J. Mol. Biol. 283 797-808 PubMed
  7. ↑ Jockovich, ME & Myers, RS (2001) Nuclease activity is essential for RecBCD recombination in Escherichia coli. Mol. Microbiol. 41 949-62 PubMed
  8. ↑ Washburn, RS & Gottesman, ME (2011) Transcription termination maintains chromosome integrity. Proc. Natl. Acad. Sci. U.S.A. 108 792-7 PubMed
  9. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  10. ↑ Salguero, I et al. (2011) RecA-dependent replication in the nrdA101(Ts) mutant of Escherichia coli under restrictive conditions. J. Bacteriol. 193 2851-60 PubMed
  11. ↑ Dermić, D & Trgovcević, Z (1999) Specific effects of a recB mutation on the HfrH strain of Escherichia coli. J. Bacteriol. 181 1334-7 PubMed
  12. ↑ Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  13. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  14. ↑ 14.0 14.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  15. ↑ 15.0 15.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

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