gyrB:Gene: Difference between revisions

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''gyrB225''
''gyrB225''
[[cgscmutation:7206|CGSC mutation ID:7206]]
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Growth Phenotype
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able to grow on beta-glucosides
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PMID:6297752
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[[cgscmutation:7206|CGSC:7206]]
arose as a compensatory mutation in the ''topA(del)'' mutant strain DM800
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Plasmid pCID549 was used to increase gene dosage of gyrB causing increased resistance toward coumermycin A1.  
Plasmid pCID549 was used to increase gene dosage of gyrB causing increased resistance toward coumermycin A1.  
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''gyrB225'' (called gyrB-225 in the paper)
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6 base pair insertion between nt 1134 and 1135<ref name='PMID:2547660'/>
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Insertion of Ala-Arg between residues 378 and 379
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Sensitivity to
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Increased sensitivity to quinolone
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PMID:11399091
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Figure 2
quinolones tested: oxolinic acid, [http://www.ebi.ac.uk/chebi/searchId.do;8786CB0A1BC3AC47A830389DBD466639?chebiId=CHEBI:138856 CHEBI:138856], ciprofloxacin, CHEBI:100241
experimental Strain: SD104-20
parental strain: SD104
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''gyrB-225''
''gyrB-225''
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6 base pair insertion between nucloetide 1134 and 1135 of gyrB.
 
see figure 1.
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2 amino acid insertion between 378 and 379 in the 43kDa N terminal region of gyr B. See fig 1.
 
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Sensitivity to
DNA relaxation
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Increase (2x) sensitivity to quinolones (Ciprofloxacin, oxolanic acid). Figure 2.  
Decreased DNA relaxation by 2 times.  
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PMID:11399091
PMID:11399091
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Experimental Strain: SD104-20


parental: SD104
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See figure 2a/b.
See table 1.  
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''gyrB-225''
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CHEBI ID:
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DNA cleavage
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DNA cleavage is reduced in mutant. Figure 5.
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PMID:11399091
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See Figure 5.
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gyrB-NI741
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oxolinic acid 138856
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Ciprofloxacin 100241
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Resistant to
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Resistant to coumermycin at 60 µg/ml.
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PMID:794878
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From strain NI708.


Parental strain: K12
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gyrB-NI748
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Resistant to
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Resistant to coumermycin at four times the regular lethal limit (60 µg/ml).
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PMID:794878
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From strain NI741 and and CRT46 dnaA
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Used as a source for drug-resistant DNA gyrase.
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gyrB-NT525
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Resistant to
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Novobiocin at 600 µg/ml.
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PMID:794878
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Parental strain: K12
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Resistance due to drug impermeability. 


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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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EcoCyc:EG10424
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[[EcoGene]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10424 ECOCYC:EG10424]
EcoGene: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]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10424 EcoGene:EG10424]
RegulonDB:ECK120000417
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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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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[EchoBASE]]
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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]]
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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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Latest revision as of 22:27, 3 October 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=NC_007779:3760296..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 mutation ID:7206

Growth Phenotype

able to grow on beta-glucosides

PMID:6297752[3]

arose as a compensatory mutation in the topA(del) mutant strain DM800

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[4]

Strain LE316

nalD mutation in strain AB1157-81

Resistant to

Mutant is resistant to Nalidixic acid (NAL)

PMID:3906038[5]

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[4]

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[4]

Strain LE316, parental strain is LE234

gyrB234(ts)

Resistant to

Coumermycin A1 resistant (at permissive growth temperatures)

PMID:94144[4]

Strain LE316, parental strain LE234

Multicopy gyrB in strain RYC1010

Resistant to

Increased resistance towards coumermycin A1

PMID:1656457[6]

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

gyrB225 (called gyrB-225 in the paper)

6 base pair insertion between nt 1134 and 1135[7]

Insertion of Ala-Arg between residues 378 and 379

Sensitivity to

Increased sensitivity to quinolone

PMID:11399091[8]

Figure 2

quinolones tested: oxolinic acid, CHEBI:138856, ciprofloxacin, CHEBI:100241

experimental Strain: SD104-20

parental strain: SD104


gyrB-225

DNA relaxation

Decreased DNA relaxation by 2 times.

PMID:11399091[8]

See table 1.

gyrB-225

DNA cleavage

DNA cleavage is reduced in mutant. Figure 5.

PMID:11399091[8]

See Figure 5.

gyrB-NI741

Resistant to

Resistant to coumermycin at 60 µg/ml.

PMID:794878[9]

From strain NI708.

Parental strain: K12

gyrB-NI748

Resistant to

Resistant to coumermycin at four times the regular lethal limit (60 µg/ml).

PMID:794878[9]

From strain NI741 and and CRT46 dnaA

Used as a source for drug-resistant DNA gyrase.

gyrB-NT525

Resistant to

Novobiocin at 600 µg/ml.

PMID:794878[9]

Parental strain: K12

Resistance due to drug impermeability.

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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[10]

Status:cloned as old JW

Primer 1:GCCTCGAATTCTTATGACTCCTC

Primer 2:CCAATATCGATATTCGCCGCTTT

3C10

Kohara Phage

Genobase

PMID:3038334[11]

3D1

Kohara Phage

Genobase

PMID:3038334[11]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[12]

est. P1 cotransduction: 95% [13]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[12]

est. P1 cotransduction: 7% [13]
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

RegulonDB

RegulonDB:ECK120000417

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948211

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. ↑ DiNardo, S et al. (1982) Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes. Cell 31 43-51 PubMed
  4. ↑ 4.0 4.1 4.2 4.3 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
  5. ↑ Hrebenda, J et al. (1985) Mutation affecting resistance of Escherichia coli K12 to nalidixic acid. J. Gen. Microbiol. 131 2285-92 PubMed
  6. ↑ 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
  7. ↑ McEachern, F & Fisher, LM (1989) Regulation of DNA supercoiling in Escherichia coli: genetic basis of a compensatory mutation in DNA gyrase. FEBS Lett. 253 67-70 PubMed
  8. ↑ 8.0 8.1 8.2 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
  9. ↑ 9.0 9.1 9.2 Gellert, M et al. (1976) Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase. Proc. Natl. Acad. Sci. U.S.A. 73 4474-8 PubMed
  10. ↑ 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
  11. ↑ 11.0 11.1 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
  12. ↑ 12.0 12.1 CGSC: The Coli Genetics Stock Center
  13. ↑ 13.0 13.1 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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