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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10424 ECOCYC:EG10424]
EcoCyc:EG10424
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10424 EcoGene:EG10424]
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Escherichia coli str. K-12 substr. MG1655  
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RegulonDB:ECK120000417
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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EchoBASE:EB0419
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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ASAP:ABE-0012093
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:32, 27 May 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

gyrB

Mnemonic

Gyrase

Synonyms

ECK3691, b3699, JW5625, Cou, himB, hisU, nalC, nalD, pcbA, parA, hopA, pcpA[1], acrB, pcpA

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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

83.53 minutes, 83.53 minutes 

MG1655: 3878142..3875728
<gbrowseImage> name=NC_000913:3875728..3878142 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3840480..3838066
<gbrowseImage> name=NC_012967:3838066..3840480 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3764061..3766475
<gbrowseImage> name=NC_012759:3764061..3766475 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3760296..3762710
<gbrowseImage> name=AC_000091:3760296..3762710 source=W3110 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

3875731

Edman degradation

PMID:3029692[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

gyrBD426N

D426N

(in nal-24, nal-102, nal-103, nal- 107, nal-108, nal-111, nal-114, en-2 and en-5 mutants; resistant to nalidixic acid and to enoxacin)

Strain variation; seeded from UniProt:P0AES6

gyrBK447E

K447E

(in nal-31, nal-109, nal-115 and nal-120 mutants; resistant to nalidixic acid)

Strain variation; seeded from UniProt:P0AES6

gyrBW751R

W751R

(in B17 resistant mutant)

Strain variation; seeded from UniProt:P0AES6

gyrBSR759RC

SR759RC

(in acriflavine susceptible mutant)

Strain variation; seeded from UniProt:P0AES6

gyrB41(Const)

CGSC:6633

gyrB226

CGSC:5052

gyrB225

CGSC:7206

gyrB204

CGSC:9714

gyrB203(ts)

temperature sensitive

CGSC:12298

gyrB221(CouR)

coumermycin resistant

CGSC:12299

gyrB234(ts)

Cell Shape

at permissive temperature (30°C), the average cell volume is larger than the gyrB+ parent (LE234)

PMID:94144[3]

Strain LE316

nalD mutation in strain AB1157-81

Resistant to

Mutant is resistant to Nalidixic acid (NAL)

PMID:3906038[4]

Strain: AB1157-81

Resistance occurs at 37C but sensitive at 30C. Refer to Figure 3 in the Paper for experimental results.

gyrB234(ts)

Resistant to

Resistant to chlorobiocin (50 ug/ml) (at permissive growth temperatures)

PMID:94144[3]

Strain LE316, parental strain LE234

gyrB234(ts)

Growth Phenotype

Temperature-sensitive growth, the plating efficiency at 42°C is less than 10-7 that of the gyrB{ parental strain LE234

PMID:94144[3]

Strain LE316, parental strain is LE234

gyrB234(ts)

Resistant to

Coumermycin A1 resistant (at permissive growth temperatures)

PMID:94144[3]

Strain LE316, parental strain LE234

Multicopy gyrB in strain RYC1010

Resistant to

Increased resistance towards coumermycin A1

PMID:1656457[5]

Plasmid pCID549 was used to increase gene dosage of gyrB causing increased resistance toward coumermycin A1.

gyrB-225

6 base pair insertion between nucloetide 1134 and 1135 of gyrB. see figure 1.

2 amino acid insertion between 378 and 379 in the 43kDa N terminal region of gyr B. See fig 1.

Sensitivity to

Increase (2x) sensitivity to quinolone Ciprofloxacin Figure 2.

PMID:11399091[6]

Experimental Strain: SD104-20

parental: SD104

See figure 2a/b.


Ciprofloxacin 100241


gyrB-225

6 base pair insertion between nucloetide 1134 and 1135 of gyrB. see figure 1.

2 amino acid insertion between 378 and 379 in the 43kDa N terminal region of gyr B. See fig 1.

Sensitivity to

Increase (2x) sensitivity to quinolone oxolinic acid Figure 2.

PMID:11399091[6]

Experimental Strain: SD104-20

parental: SD104

See figure 2a/b.

CHEBI ID:

oxolinic acid 138856


gyrB-225

DNA relaxation

Decreased DNA relaxation by 2 times.

PMID:11399091[6]

See table 1.

gyrB-225

DNA cleavage

DNA cleavage is reduced in mutant. Figure 5.

PMID:11399091[6]

See Figure 5.

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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

JW5625

Plasmid clone

Shigen

PMID:16769691[7]

Status:cloned as old JW

Primer 1:GCCTCGAATTCTTATGACTCCTC

Primer 2:CCAATATCGATATTCGCCGCTTT

3C10

Kohara Phage

Genobase

PMID:3038334[8]

3D1

Kohara Phage

Genobase

PMID:3038334[8]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[9]

est. P1 cotransduction: 95% [10]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[9]

est. P1 cotransduction: 7% [10]
Synonyms:zie-296::Tn10

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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:EG10424

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10424

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948211

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000417

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0419

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012093

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. ↑ Adachi, T et al. (1987) DNA sequence of the E. coli gyrB gene: application of a new sequencing strategy. Nucleic Acids Res. 15 771-84 PubMed
  3. ↑ 3.0 3.1 3.2 3.3 Orr, E et al. (1979) Isolation and characterisation of a strain carrying a conditional lethal mutation in the cou gene of Escherichia coli K12. Mol. Gen. Genet. 177 103-12 PubMed
  4. ↑ Hrebenda, J et al. (1985) Mutation affecting resistance of Escherichia coli K12 to nalidixic acid. J. Gen. Microbiol. 131 2285-92 PubMed
  5. ↑ del Castillo, I et al. (1991) An unusual mechanism for resistance to the antibiotic coumermycin A1. Proc. Natl. Acad. Sci. U.S.A. 88 8860-4 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 Heddle, JG et al. (2001) gyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity. J. Mol. Biol. 309 1219-31 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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