Cis Element:dif
Cis element summary table
| Standard Name |
dif |
|---|---|
| Synonyms |
deletion-induced filamentation |
| Function |
Recombination site in terminus |
| Location |
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| SO terms |
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Notes
Location and Sequence
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 |
|---|---|---|---|---|
|
34.2 minutes |
MG1655: 1588774..1588801 |
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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
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| Partner Type | Partner | Notes | References | Evidence |
|---|---|---|---|---|
|
Protein |
XerC |
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Protein |
XerD |
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Notes
Sites where XerCD bind and cleave dif can be found in Blakely et al. (1997)[7].
Mutant alleles and phenotypes
| Allele | Nt change(s) | Phenotype: Type | Phenotype: Description | Reference | Availability | Comments |
|---|---|---|---|---|---|---|
|
Δdif |
Growth Phenotype |
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Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
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pSDC124 |
Plasmid Clone |
pUC18-based dif reporter |
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pFC238 |
Plasmid Clone |
pGB2-based dif reporter |
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pFH127 |
Plasmid Clone |
pGB2ts-based dif reporter carrying one dif site |
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NL Strains |
Strain |
This paper lists a variety of different dif deletions and other constructs designed to test the dif locus |
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pUC-dif |
Plasmid Clone |
pUC18-based dif reporter |
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GR35 |
Strain |
AB1157difΔ6 |
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GR47 |
Strain |
AB1157lexA3difΔ6 |
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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[12], or dif-Km-dif excision assays[13]. Steiner and Kuempel (1998) used a density label assay to analyze dif recombination[14].
Accessions
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
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Notes
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 5.0 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
- ↑ 6.0 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
- ↑ 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
- ↑ Blakely, G et al. (1991) Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol. 3 789-98 PubMed
- ↑ 9.0 9.1 9.2 Recchia, GD et al. (1999) FtsK-dependent and -independent pathways of Xer site-specific recombination. EMBO J. 18 5724-34 PubMed
- ↑ 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
- ↑ Grainge, I et al. (2007) Unlinking chromosome catenanes in vivo by site-specific recombination. EMBO J. 26 4228-38 PubMed
- ↑ Yates, J et al. (2003) Species specificity in the activation of Xer recombination at dif by FtsK. Mol. Microbiol. 49 241-9 PubMed
- ↑ 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
- ↑ 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