Cis Element:dif

From EcoliWiki
Revision as of 20:22, 1 July 2010 by Azweifel (talk | contribs) (Table edited by Azweifel via TableEdit)
Jump to navigation Jump to search

Cis element summary table

Standard Name

dif

Synonyms

deletion-induced filamentation

Function

Recombination site in terminus

Location
  • 34.2 minutes in MG1655
  • 33.6 minutes in AB1157 [1]
SO terms


edit table

Notes

Location and Sequence

[back to top]


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

34.2 minutes

MG1655: 1588774..1588801
gbrowse_img.php?coord=1588774..1588801&genome=ecoli&name=MG1655&trackset=DNA_unlabeled&width=300&.png

edit table


Notes

The dif site is a 28bp sequence located within a 30kb region of the terminus known as the "dif activity zone" (DAZ) and is involved in Chromosome Dimer Resolution involving XerCD[2][3][4]. dif must be located in the terminus region for proper function and may be functionally replaced by loxP if the Cre recombinase is supplied in trans[5].

Interactions

[back to top]


See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

XerC

PMID:11114887[6]

Protein

XerD

PMID:11114887[6]


edit table


Notes

Sites where XerCD bind and cleave dif can be found in Blakely et al. (1997)[7].

Mutant alleles and phenotypes

[back to top]


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

Δdif

Growth Phenotype

Filamentation- >15% of cells

PMID:15065657[8]

Δdif

Growth Phenotype

  • subpopulation of filamentous cells with abnormal nucleoids
  • induction of the SOS repair system

PMID:1657123[1]

Δdif rarA

Growth Phenotype

Filamentation- >15% of cells

PMID:15065657[8]


edit table


Notes

Genetic Resources

[back to top]


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

Resource Resource Type Source Notes/Reference

pSDC124

Plasmid Clone

pUC18-based dif reporter

PMID:1931824[9]

pFC238

Plasmid Clone

pGB2-based dif reporter

PMID:10523315[10]

pFH127

Plasmid Clone

pGB2ts-based dif reporter carrying one dif site

PMID:9067608[11]

NL Strains

Strain

This paper lists a variety of different dif deletions and other constructs designed to test the dif locus

PMID:7729430[5]

pUC-dif

Plasmid Clone

pUC18-based dif reporter

PMID:17805344[12]

GR35

Strain

AB1157difΔ6

PMID:10523315[10]

GR47

Strain

AB1157lexA3difΔ6

PMID:10523315[10]

edit table

Notes

  • One way to test the resolution competency at the dif activity zone (DAZ) or individual dif sites is to perform plasmid dimer resolution assays[13], or dif-Km-dif excision assays[14]. Steiner and Kuempel (1998) used a density label assay to analyze dif recombination[15][16].

Accessions

[back to top]


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

Database Accession Notes

eric

dif


edit table


Notes

References

[back to top]


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

  1. ↑ 1.0 1.1 Kuempel, PL et al. (1991) dif, a recA-independent recombination site in the terminus region of the chromosome of Escherichia coli. New Biol. 3 799-811 PubMed
  2. ↑ Tecklenburg, M et al. (1995) The dif resolvase locus of the Escherichia coli chromosome can be replaced by a 33-bp sequence, but function depends on location. Proc. Natl. Acad. Sci. U.S.A. 92 1352-6 PubMed
  3. ↑ Cornet, F et al. (1996) Restriction of the activity of the recombination site dif to a small zone of the Escherichia coli chromosome. Genes Dev. 10 1152-61 PubMed
  4. ↑ Kuempel, P et al. (1996) Use of a transposon (Tndif) to obtain suppressing and nonsuppressing insertions of the dif resolvase site of Escherichia coli. Genes Dev. 10 1162-71 PubMed
  5. ↑ 5.0 5.1 Leslie, NR & Sherratt, DJ (1995) Site-specific recombination in the replication terminus region of Escherichia coli: functional replacement of dif. EMBO J. 14 1561-70 PubMed
  6. ↑ 6.0 6.1 Barre, FX et al. (2000) FtsK functions in the processing of a Holliday junction intermediate during bacterial chromosome segregation. Genes Dev. 14 2976-88 PubMed
  7. ↑ Blakely, GW et al. (1997) Binding and cleavage of nicked substrates by site-specific recombinases XerC and XerD. J. Mol. Biol. 265 30-9 PubMed
  8. ↑ 8.0 8.1 Sherratt, DJ et al. (2004) Recombination and chromosome segregation. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 359 61-9 PubMed
  9. ↑ Blakely, G et al. (1991) Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol. 3 789-98 PubMed
  10. ↑ 10.0 10.1 10.2 Recchia, GD et al. (1999) FtsK-dependent and -independent pathways of Xer site-specific recombination. EMBO J. 18 5724-34 PubMed
  11. ↑ Hayes, F & Sherratt, DJ (1997) Recombinase binding specificity at the chromosome dimer resolution site dif of Escherichia coli. J. Mol. Biol. 266 525-37 PubMed
  12. ↑ Grainge, I et al. (2007) Unlinking chromosome catenanes in vivo by site-specific recombination. EMBO J. 26 4228-38 PubMed
  13. ↑ Yates, J et al. (2003) Species specificity in the activation of Xer recombination at dif by FtsK. Mol. Microbiol. 49 241-9 PubMed
  14. ↑ Pérals, K et al. (2000) Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity. Mol. Microbiol. 36 33-43 PubMed
  15. ↑ Steiner, WW & Kuempel, PL (1998) Cell division is required for resolution of dimer chromosomes at the dif locus of Escherichia coli. Mol. Microbiol. 27 257-68 PubMed
  16. ↑ Steiner, WW & Kuempel, PL (1998) Sister chromatid exchange frequencies in Escherichia coli analyzed by recombination at the dif resolvase site. J. Bacteriol. 180 6269-75 PubMed

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=Cis_Element:dif&oldid=1167522"